You can't fill it in the VAB or SPH. You have to put a pod on it somewhere and crew the pod, then you EVA the Kerbal, right click on the seat and click "board." Then you can jettison the pod. So you weren't doing anything wrong. You just can't put Kerbals in seats directly from the VAB/SPH. However, there is a mod called "Take Command" that allows you to do this. I think it should be stock.
Okay. First of all, Kerbal Space Program has its limits, and that space station must be hundreds of parts. I am sorry to say this, but it has gotten a bit too big.
My biggest rocket ever was something around 750 parts. It had a time dilation of 8 to 1.
The point is, use less parts. The modules I see are ten times as complicated as they need to be. So, when building huge things, try to make each module minimalist. Use only what you need. You don't need twenty ladders and 8 rcs tanks on each module.
That being said, I applaud your determination at building something that huge!
Tips for optimizing part count:
Use a stack battery instead of a lot of radial ones
Use a stack RCS tank instead of lots of radial ones
Put stuff like RCS ports and extra SAS units on decouplers, so you can jettison them and delete them from the tracking station.
You don't need external ladders. If you do need them, use deployable ones.
Those hub modules don't need to be that complex either. Unless you are set on that design.
Build your stations above 250Km. This reduces lag.
I hope I helped!