Near as I can tell, you have to look at the monster and figure out what its ECL is; that, of course, is Hit Dice + Level Adjustment (LA). You can either figure that out yourself from Savage Species, or download the MM2 3.5 update, which does include LA for MM2 creatures.
Next, you figure out a class progression, by splitting the LA levels amongst the HD, as evenly as possible.
You first need to figure out how much stuff the 1st-level monster class has. I *think* the guideline is that the 1st level can't have more stuff attached than would a regular 1st-level humanoid character. I don't recall that being stated, but it makes sense.
Then, you go and divide up the ability score modifiers, mutant powers, etc., among the class levels. Remember that, since you have class levels that are purely LA, you might want to seed the powers on those levels a bit more, so the character feels like they get something. Put the higher-level powers towards the end of the class progression, and be sure and spread out the ability score modifiers.
Hope this helps. (Probably not, but hey...)
Brad