1) What is a good idea is to set a unit cell that allow you to create all the set of caps...don't run away from this choice, it's the correct one.
2) The problem is the huge leap between your smallest and your biggest cap, there's no alternative, your unit cell MUST be 1fF...
3) From what I see in the picture, the distribution, at first sight, seems to be okay. For sure you'll have an interesting routing job...
4) Something I would add is POLY (you're using POLY caps, right?) all around teh complete structure and between the caps (it will create a POLY GRID, with the caps inside every single grid square).
This is oriented to avoid process etching issues when processing the part.
Hope this helps.