I'm still a bit new at this myself, but I'll have a go at your questions.
Question One --- Can more than one star base operate in the same area; if I have two economic star bases that cover the same planet does it get a larger bonus than if I had only one? ---
From kryo himself in an old post.
Yes, Starbase bonuses stack in overlapping areas of effect.
You can select both bases using CTRL+Click+And+Drag.
This will highlight the areas they affect. The areas where they overlap will be brighter. This can help you spot those "sweet spots" where you get a bigger bonus.
Question Two --- If I have multiple star bases covering a trade route will that lead to larger trade bonuses?
See answer to question one.
Question Three --- Still being a noob it seams like a good idea place one of each star base in each sector I have, it this wasteful?
I'd have to say that this question is very dependent on what the situation in the game is. Typically you won't need a Military base near your core worlds if there aren't going to be any attacks in that area any time soon. The same for Influence bases which extend your influence in a certain area of effect. If you place it right in the middle of your own planets...its kinda going to waste (unless you are protecting yourself from someone elses Influence Bases).
Question Four--- Is it a good idea to have military star bases with different weapons over lapping each other to be effective against all defenses?
If the base is near one opponent focusing on one defense/attack, then don't bother with all 3 just focus on stopping his attack and hitting him with something that isn't his defense. That said, if you can fit you have the constructors to put the moduals on there, go for it.
Question...well Statement... Five --- requirements to get access to bigger ships.
Make your own ships

. Its much cooler then using the stock crappy ones. If you mean hull sizes, those upgrades come at Medium Scale Building / Large Scale Building and Massive Scale Building.
If you have any further questions please try using the search function for a while first

. Or check out the Galactopedia. The link for which I have misplaced...