1). Yes. When you cilck contribute, you get a slider to adjust how much you want to give. Same with most inputs, exceptions being data samples and duty officers. Data samples you get a list of all your samples in inventory or bank, with a slider on each one. Duty officers you get a list with checkboxes, and you select all the ones you want to contribute.
2/3). All fleets have starbases, as well as New Romulus embassies, but they're all through the same "door" so there's no clutter. All fleets access their starbase through the Starbase system in the Eta Eridani sector block. The Federation one is at the bottom-left of the block, Klingon at the top-right. When you enter that system, you're sent to your fleet's starbase exterior, and can beam down to its interior.
Likewise with the embassy - every fleet's embassy is through the doors at the top of the stairs at the north end of the New Romulus staging area, or by beaming down from orbit.
In both cases, you can only see another fleet's holdings by invite from a member.
For fleet missions, the holding you see is either the one belonging to a random member of the group (if it's a pug) or the queue owner's (if it's a private queue).
If you're in a large fleet, I'm sure plenty of people there would be happy to provide you with answers to all the questions you have about the game and the fleetbase in particular. Afterall, that is what fleet members should do, help one another with the game.
Having said that, here's the answers to your questions:
1) How can I contribute a set amount of dilithium to certain projects without donating all the dil I have?
When you click contribute, you can use the slider to donate theamount you wish, you don't have to donate all of it. The slider is not extremely precise, but does the work.
2) Where is the information as to where my fleet starbase is?
You fleet base is located in the Eta Eridani Sector, once there click M to see your map (or system list) and locate it, I think it's called Federation Starbase (or something like that)
3) Do all created fleets all have different starbases??? Wouldnt that mean tons of starbases everywhere?? That doesn't sound right.
Yes, and No. All fleets have a starbase, but they're all at the same location. All starbase are the same model, but some have unlocked features (visual display, bank access, stores, etc.).