template plastic is a bit different than stencil plastic- stencil plastic is often cut with a stencil knife- which heats up- melt-cuts the plastic- template plastic is often made to not melt so you can touch your applique templates with an iron- so that may be part of the problem you had-
there is also a little swivel knife (available at Nancy's notions) that works great for getting into those tight little places it is one of those tools i don't know how i lived without- i use it so much! and very inexpensive. (i think on the pages with rotory cutters & tools in her catalog) i have the swivel knife and the mini rotory cutter- both are used alot when i am cutting out appliques.
as for marking quilts i generally use chalk- you can brush or wash it off - it shows up well- is available in lots of colors- works for me.