This depends very much on the schematic connectivity of the array. If all caps share one common node - which is often the case - I'd suggest to make it the common bottom node. If you have an array of many single equal devices, of course it would be wise to have the same number of each in every row & column. This of course is not possible in your case. Here, a 2nd criterion comes up: Best possible distribution, which is your 2nd suggestion. However, the connectivity of the array also contributes to the asymmetry of the whole array. This asymmetry also must be held low enough, and this is probably easier with your 1st suggestion.
After layout you should check (simulate) the extracted netlist until its asymmetry (including connections to the rest of the circuit) is below your required value.