The technique you mention is called Appliquilt, a technique published in some books by Tonee White. You may be able to find more information by doing a search on Appliquilt on the QB (see the search box in upper righthand corner). In any case, it should be do-able.
I'm not sure stippling through appliques would work very well, as in addition to the 4 layers (applique, backing fabric, batting, backing fabric) you would be going through the fusible. If you use a very light fusible such as Misty Fuse, it would not be a problem; however, heavier fusibles could cause a lot of problems.