How to Design Tech Trees ?

That's a pretty vague question, and you might need to be a little more specific.. What sort of trouble are you having now? What sort of tech tree are you looking at making?

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The first step is to determine what style of tech tree you want to have.. Here are some various paradigms I have seen/contemplated in the past. Certainly, there are other systems one can conceive, as well as hybrids of these 7.

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1) SEIV style bush, or perhaps a field of grass. There is a shallow base of generalized theoretical tech areas (physics, construction, military science, etc.) with a huge number of wholely unrelated applied areas branching off from that.

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2) Ascendency/Civ style intertwined tree where you generally only have 4 to 6 tech areas available at a time. Varying combinations of current techs open new techs to be researched.

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3) MOO/MOO2 style "tree" with 8 or 10 general areas (physics, chemistry, construction, etc.). All items fall under a specified level of one area or another. MOO2 also had a weird setup where each level had various items available, and you could only choose one of them as your researched result (the others had to be traded with other empires).

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4) An actual tree shape loosely in the SEIV style. Most tech areas give only one (or two highly related) items. Unlike SEIV, more advanced techs generally require research in lesser areas.

Such a tree should have a tall trunk, aka lots of items in the core. Branches should come off at varying heights (10+ levels of theoretical techs with lots of things coming out at most levels). Different parts of the core can merge together to support the large branches (Physics + Chemistry = some general area of weapons techs, perhaps High Energy Discharge Weapons). Each branch would have smaller branches coming off (specific applications of the general areas, perhaps Ripper Beam vs. Incinerator Beam vs. Wave Motion Gun, as different tech areas branching from High Energy Discharge area). You can even have things at the very far ends merge back together for combinations. Think different levels of leaves from different branches combining to create a unified shade layer or something.

Take Armor for a more concrete example. In the early game, you might have an "Armor" tech area that provides only basic Armor components. With enough theoretical science reseach and research into Armor, some new tech areas will become available. They might be Stealth Armor, Emissive Armor, and Scattering Armor. Scattering Armor might require some research into ECM technologies. Cloaking technologies could require a few levels in Stealth Armor, in addition to the other theoretical areas (Physics 3 in SEIV). This illustrates some tech branch interleaving.

This option creates more of a branching tree, unlike the SEIV bush.

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5) Technologies are broken up into ages, similar to Civ 3/4. You can research many areas up to a certain threshhold, then they stop. You'd get armor, shields, engines, weapons, resource miners, etc. to a certain level. Once you get enough techs to a certain level, a new "age" or "era" becomes available. This allows new tech levels in most (or all) fields to become available, preferably as new tech areas rather than just continuations of old ones.

One variant could be to have ages require, say, 7 out of 12 tech areas at level X. This would allow different paths to be followed by different empires to progress to the next age, thus increasing strategic diversity.

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6) Compacted system where loosely related items are combined into a smaller number of tech areas for simplicity or for higher level "congressional" management, abstracting contracting the research to research firms.

It is like creeping vines genetically engineered to produce 12 different species of fruits from each vine.

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7) A tech grid style research tree. You have the normal research areas for engines, hulls, weapons by type, and missiles by type and so on. Then you have enhancing research areas that will enhance one or more components, factories, weapons, etc. Effects fo these enhancing techs would include reducing size, cost or supplies used, increasing range, damage, structure points, and so on.

Note that a tech grid could be done in most other styles of research (for example, MOO2 reduced component costs and sizes from a given area as more levels were researched), but its a notable enough design paradigm to warrant special mention.

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You could maybe even mesh this with a race specific dimension, which would trigger tech discoveries only your race can get, while still forcing you to research more than just a specific racial tech branch in order to unlock interesting stuff. So if I were a crystalline race and research medium hulls I might discover a special hull type which a symbiont race would not. It's a step away from the crystalline and organic race bonusses you get in the BM mod, where this is a given even without researching organic technology.

In addition to "shape" of the tech tree, figure out the most basic of components.
What theoretical technologies are required to gain access to Ships? Fighters? Drones? Satellites? Mines? Weapon(s) Platforms?
{EX: Material Science lvl 1 and Construction lvl 1 to gain access to Starships and Starbases.}
[EX: Construction, alone, reduces size of facilities. Industry makes facilities more effective, and Material Science allows different resource-costs, (EX: facility could cost mostly Mineral or mostly Radioactives) improves durability, and allows access to (assuming they aren't racial) Crystallurgy, Biological Manipulation, and (possibly) Metallurgy.]

Once you have those figured out, then come more difficult ones:
Which Theroretical, Applied, or multiple Techs lead to what Weapons, Armors, and Shields?

Then an even meaner question.
Which of the previous techs are Racial Traits? It's best to save this for last, as you may decide that Racial Traits are really just Shortcuts to given techs.
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I'll make one later.

Write it all out along with any prerequisites ahead of time. I found it was easy to get lost sometimes and forget things.