The tool I use the most for applying automotive body putty to my models is an artist's pallate (sp) knife. I have three of various sizes and blade shapes (and it isn't that hard to modify the shape to one that will work better for you). They can be found in art supply stores, Hobby Lobby, Michael's and even some hobby shops and they cost from three to twenty bucks depending on size and shape (and of course manufacturer) Don't know what i would do without mine.
I've used 3M laquer based Spot & Glaze for years and if you don't put on too much one time, have never really had any problems with it melting or deforming the plastic. Instead of applying one big glop to an area, apply a thin layer, sand it down, apply a second layer and sand and so on until the area you want is filled. Also shrinkage is greatly reduced if you do this. I've also tried 3M Acryl Blue but don't really care for it as it seems to dry too fast and doesn't hold near as well as the laquer based putty. If you do decide to go with these putties, would recommend that you buy a small tube to try it, and if you like it, buy the largest tube you can get. As long as you make sure the top is back on tight each time you use it, it should last between 5 and 7 years.