I am beginning to paint my 2nd starter box. Will it help to paint the bases or minis differently to separate the different units from the first starter box units? In order to help identify them for gameplay? Or would it help to actually make them all more uniform so they're easily interchangeable?

Depends, are you playing different armies?

If it is one army, then no. I painted a ring around my army bases a different color for each squad.

No 2 units oc stormtroopers are done the same out of the 2 cores. All are different color or stripe combos. I wanted easily identified units and something besides mono white imperial army.