Paint a Roman Letter I, II , III, IV... on one corner (if you use rectangular) of the Base and put the Number into your List so you can make it to what ever you want. Or use small colored dots which you paint on the flanks of the Base
and make the Flagship 4 white Dots, Leader of the 1st Squadron White white red and so on. Use only Colors that are easy to identify.
If you use 1/1200th Models you can place the above on the Aft edge of the Base...this will be the most often seen Side of your Vessel