I use Tamiya primer, it does smell horrible, but is amazing. I have not had any problems with MM Acrylic paint over this, but it is a tricky paint to work with.
For landing gear, doors and all the other little bits, I normally paint them seperately and then add at the appropriate time with either super glue (CA) or something like tenax 7R with a touch and flow applicator.
For my canopies, I dip in future and let cure first, then mask, prime, paint as needed, etc. Only once the weathering and dull coats are on do I peel off the tape. For the longest time I was loathe to by the tamiya tape due to cost, but I have found it to be well worth the money.
For weathering and washes I use artists oil paints mixed in white turpentine after a good gloss coat is on over the decals. The gloss coat makes the oil paints flow farely well and since one is acrylic ( I use future for my clear coats) and the oil is enamel based there is not much of a reaction. Once I am finished with the weathering I seal up the paint with an acrylic flat coat and remove all the masks.
Hope that this helps.
<Matt