I tried launching through OMM which was running as an executable through MO, but no dice, as soon as the game was started it said OBSE wasn't active. I didn't actually try just running the game through MO but I'm assuming that won't work? (No longer at my PC).
Oh, and another question, I read that to install mods with an omod installer, the preferred method is to run OMM as an executable and then run the omod through that as normal. Is this right? I tested it out to check if OBSE was working by installing Supreme Magicka, and it put the files it installed in the overwrite thing, so presumably if I do it that way, I need to close OMM after installing each mod? Is there a better way to do it, should I just use the "manual" install option in MO (I.e. the bit where you look at what's in the archive and can set the data directory if it's wrong and so on)? I'm not planning to use a huge number of mods, but a few do have a lot of files and options (Better Cities, for a start.)
I'm sure I'll have more questions, and thanks to anyone who's taken the time to read (and answer, if applicable).