Unfortuanately I was in a similar situatation, although it was with my Dads partner and the problem there was she felt jealous/threatened by me (more so than with my Mother consdering my parents have remained good friends). So you have my full sympathy it's an awfull position to be in.
I agree with Peace talking to your Mum etc is the best place to start, and just take it from there and see what happens. Sadly that's all the advice I can really give you as my problem was solved by them spliting up (she turned out to be quite a nutter!!) and my Dad living with us for 18 months!
So good luck and big hugs for now!!