It is actually very simple other that the horrible nature of the constantly changing emulator versions and the requirement that the roms themselves must match the version of the emulator. (That said, yes, older roms haven't changed much or at all and that is why you can always test with something like pac-man to get started since it will probably work on just about every MAME version).
1. Download the .78 version of your roms
2. Stick them unzipped in the Arcade (or mame-libretro) folder (if the zips are in one big archive, unzip the archive to get all the zipped roms)
3. Make sure in RetroArch that you have installed the lrmame-2003 core
4. Run EmulationStation and you should see all your roms in either Arcade or Mame, depending on where you put them (I recommend Arcade)
5. Run a rom like pac-man or 1943
You will need a few more things to get this working better, such as samples that go in your samples folder. Donkey Kong, for example will be missing the shoe squeak when Mario runs and the "boom, boom, boom" sound when Kong stomps and makes the girders fall. The samples will provide the missing sounds for the roms that need them.
You can run other versions of MAME on the Pi, but the 2003 version is the best compromise of speed, size and compatibility. I think it runs most of what anyone really needs as far as arcade classics. What it doesn't run, I change on a rom by rom basis. This is what works for me and it is only slightly tedious:
1. I have several rom sets for different versions of mame (I also have a powerful PC and have a different setup)
2. I use the .78 romset and the lrmame2003 as my default emulator in RetroArch for the Pi3b
3. I put all Arcade games in the Arcade folder
4. I keep a spreadsheet to track all the exceptions to the default setup which are:
a. I overwrote all my X/Y vector games (tempest, battlezone, etc.) with .106 versions and set a rom by rom exception to use AdvanceMAME 3.6 (trust me!)
b. I use a rom by rom override for certain .78 roms to use other emulators that run better, faster, etc. for that rom and record that change
So I need to know which roms are what versions since I mix them up a bit and because I put everything in the Arcade folder rather than some in one Mame folder and others in another Mame folder and some in a Capcom folder, etc. Up to you though how you organize folders.