Nice thing to do with a supply freighter ...

Interesting.
Possibly impractical and likely to cause some problems when it comes to lost cargo and repairing damage. Seems like a posible bad thing if you are needing to use freigthers to protect carriers, since carriers should be the ones protecting themselves and the freighters using their fighters.
I do understand the basic concept, I try to fit at least 1 gun and 1 PD on my freighters when possible, but more for last resort than for actually attack the enemy.

Alternitive.
Speaking of carriers, toss on some fighter bays on a freigther hull, and load up some rocket pod equipped fighters. A few rocket pod hits will hurt the enemy a lot more than some lone DU Cannon the freighter has for defense. Any fighter losses will be worth it if you manage to take out a few engines on the enemy ship and make it impoissible for them to catch the freighter.

Similarly, satellite bays, and some CSM/large mount gun equiped sats.
Either way, just need a variant of 'don't get hurt' with 'launch all units' set to true, or just use 'don't get hurt' and launch manually if doing tactical combat.

Another alternative.
Use regular ship hulls, cruiser or smaller, for 12 engine ships with less cargo pods than a freighter, but packing a good deal more weapons and armor due to not having to waste 50% of space on cargo components.

are you sure that it makes a difference where the engines are located? i thougth it is random which components of the outer hull are hit first.

I also thought it was random.

I have heard there was a mod that adds in directional damage, but that's about it.

I'm playing stock, and I don't recall anything about damage being directional, components seem to take damage at random when I test out designs in the simulator.

I have heard someplace that the order you put components in might have an effect on the order that items take damage in, but I don't know how true that is.

I like to have some fighters on hand, even if it is a hassle making them for every planet I have and a dozen or so fighter carrying transports.

My primary Troop Transports (rarely actually used as such) are escort carriers in their own right, and made to be multi-taskers.

Here is the basic setup, a lvl 10 cruiser.
The basics (bridge, 3 life support, 3 crew quarters), basic sensor auxiliary control, 12 engines, 80kt armor (I include a stealth armor), 60kt shields (I use 1 phased shield and 1 regenerator), 2 cargo bays, 4 fighter bays, 2 drone launchers, 2 mine layers, 2 satellite bays, combat sensor, ecm, medical bay, security station, self destruct, tachyon scanner, long range scanner, mine sweeper, cloaking device, 2 PD beams, 2 anti-proton beams.

With high enough tech in the right areas, you can get a good 4,000+ kt of cargo space, a solar collector/quantum reactor and an ordnance vat.

My tech is high enough with the game I originally made it in that I only need 1 each life support and crew quarters, so I used a spare 40kt for a quantum reactor and an ordnance vat.

Handy multi-tasker, and well suited for operating in/near enemy territory, especially with/as escort

You could take off some of the stuff (scanners, mine sweeper, cloak) and put on more weapons and shields for a more combat oriented ship, upgrade the anti-proton beams (or other 2x30kt or 3x20kt weapons) to heavy mounts along with adding a Flak Cannon or Bomblet Missile (or other PD gun and more armor, or other components), or even to add in more cargo hauling capacity.

I like to use the basic multi-tasker for all sorts of things, and whereever I have a Cruiser sized spaceyard ship, one will be with it.

I use the one flxible design I described because it helps to cut down on the number of ships I need for some situations. It would simply be impractical to have to build a carrier, satellite ship, mine layer and drone carrier for a space yard ship just to deploy any units it builds while in other systems.

A few of my ships are basically variants of other designs, like being satisfied with the defense potential of a destroyer made for exploration, scouting and screening warp points, and replacing the non-combat/support type components (scanners, mine sweeper, etc) with extra weapons and end up with a nice defense ship, or updating an old frigate design to be an annoying cannon fodder/support ship for big/slow ships packing long range weapons. Toss in the neural combat net to make newly made cannon fodder ships benifit from more durable big ships with more experienced crews.

I have a lot of ship designs myself, some flexible, some focused on just one or two things, along with ships of different sizes. I even got a Cruiser sized ship flying around with a few Quantum Reactors, Ordnance Vats, Supply Storage and two Repair Bays, to act as a mobile support and resupply platform for my many ships/fleets away from home, along with a variant that removes the repair bays for some extra supply/ordnance capacity, an extra phased shield, extra gun, and a little more armor, to make it a major pain in the butt for enemies to take out. It could cause major problems for the enemy when you can refuel, reload and repair your ships while on their front doorstep.

That's a nice looking fleet setup.
Since it's an offensive fleet, when you get the resources make sure to have at least 2 of each ship setup for important tasks, such as scanner ships and repair ships.
I make sure repair bay and space yards are at the top of the component repair priority list, so it gets extra repair capacity going asap instead of trying to repair other stuff first.

A few other ideas/suggestions.

When you get the tech, add in a space yard ship or two.
They can be handy for various reasons.

To suppliment supply ships, a supply sat.
Toss in something like 2-3 solar collectos and some supply storage on a satellite. Handy for extra supply production if your fleet isn't going anywhere for somereason, or even to hide in a non-damaging storm or an asteroid field in other systems along with a sat with sensors/scanners, and a few armed sats for protection.
When they become available, quantum reactors allow sats to stay supplied in systems without stars.

On the subject of satellites, use the multi-purpose transports to drop the little buggers in all sorts of places. To protect some point of interest (like a planet with ruins, or any planet they enemy could colonize), on a warp point (in their system, in a system with no planets to pot shot enemy ships that come through or that try to go through), simply to annoy the enemy in any number of ways (like a sat with few guns and many shields/armor/defense bonus giving components), drop them on a warp point while your fleet is leaving their system to hinder pursuit, etc.

My q-ships are even simpler. Put on a shield, 2 fighter bays and 2 pd. Load up perhaps 6 fighters. If you are going through unknown or bad territory, send the freighters in groups. If you are doing short hops through friendly territory, you can forget about the fighters and use the f-bay cargo space for whatever. I also like doing this to colony ships, and they carry a couple mines for post landing.
The fighters are cheap and will at the very least slow down any ship chasing your freighter. If the fighters can't handle whatever it is, your equivalent armed q-ship would not survive anyway. This way you have a better chance of getting your cargo to the destination.

"Genius is Simplicity" chris connors
"To win without fighting is best" sun tsu
those who think they know everything are annoying to those of us who do