The innovation complex is a super projects unique to the terran tech tree. It has something to do with ship speed... I believe that it gives +1 speed to all ships built on the planet, which is a very nice early game boost.
Yeah, you can only build one. You'll probably want it on earth, and you'll want to get it early so you can take advantage of the additional speed in the colony rush.
As for what bonus tiles will effect it, the short answer is that it benefits from none of them. The longer answer is that on the planetary build screen, you can select any building and look at the window on the bottom. In that window, it will tell you exactly what bonuses the improvement will give. If it gives research points (not a research percent) then research tiles will amplify that. Likewise with manufacturing or influence. If a building gives multiple types of bonuses (like the Thalan Hyperion Matrix) then a bonus tile will only affect the stat it is meant to affect.