Woot, Woot..
Most people are getting spoiled with MO. In reality OBMM and especially WyreBash are some pretty dam stable and functional mod managers. They are tanks in the mod managing world. Essentially the difference is they actually load the mods (and unload them) directly from the data folder. If you find something needed to be loaded afterwards. No problems just reinstall it. (as opposed to MO move up or down on the left side. ) That is essentially that. Mo has some useful tools to see conflicts in real time etc but WyreBash does to (I believe it does at least :P)
From my understanding of the process MO isn't liking the Steam version of Oblivion. When this happens there isn't the same level of responsiveness or stability. Scripting mods for example likely will never fire. It is also likely that complex install instructions (installers etc for Bash, Obmm etc) won't fire properly as MO won't know what to do with the mods and instructions as it don't see or recognize the exe. Finally one manager with occasional use of another one then packaging the results up is fine when needed but the entire list of mod not only from one manager but from two different managers... fail to package up everything properly. and you will have hell to pay to find wont what went wrong and OBMM and I suspect WyrebAsh will start to freak if it don't see the files anymore (after they have been packed) like FOMM does or did.
Now the best thing to do is encourage MO development to address the Steam and OBSE connectivity/recognition issues so that we can install them properly along with proper OBMM support to install Oblivion mods as well. (provided that isn't currently functional)