Out of curiosity, what happens you setup a multi memory card and then you fill it up? Can you crate another multi memory card?
I used a multi memory card because I wanted to copy saves to it from the internet and couldn't easily do this with individual memory card files (it wouldn't work).
EmuMC works exactly like a real one, when it's full it's full, if you fill it then you have three options:
-Upgrade to a bigger size "I don't recommend anything bigger than 2 MB though I use 8 MB and it works just fine, just don't use 16 MB as it causes a lot of issues
-Create another EmuMC and keep switching back and fourth "by renaming the files, you can use Wii Xplorer to do it on the Wii on the fly" or just use individual EmuMC for each game
-Delete your old saves that you no longer want, you can either use Dolphin or if you have the GC Bios you can just use that to delete your saves from a EmuMC
These are your only solutions, despite the fact I use MultiMC for I prefer it this way I recommend using indivisual MCs "500 KB each to save space less the game required more space for extra data and such" to be on the safe side, it's also good because if you corrupt a save it'll only affect said game and not the rest of the saves you have.