I have most every thread but this issue doesn't seem to be addressed. Most threads either discuss just plates or plates and insert soft armor.  I want to purchase a 3A vest and some plates. I want to be able to place the plates into the carrier and then the carrier over the vest.

What are some issues I should be aware of when setting up this system?

Is there a carrier or a class of carrier that is best for this setup?

TIA

Are you talking about something like this:
PACA Low Vis concealable carrier for SPEAR BALCS

I'm not sure what your looking for?  You can get a vest like cops wear to be worn under or over your shirt.  You can than get a plate carrier to wear over that.  I think most threads have dealt with all the options.  Beware that most concealable vest are cut short for wearing with a duty belt & sitting without the vest choking you.  If you want non- concealable soft armor, look for an interceptor or some type of tactical stlye vest.  These are usually cut longer and add extra coverage (side, neck, shoulders,etc.).  Probablly not the best vest to have to sit or drive in.  Eagle makes a great plate carrier as does HSGI (wo,wa,we).  There's alot of option you can go with.  I pretty much have them all.