Converting MTS for best use in After Effects?
Use ClipWrap to convert the MTS file into a Quicktime Movie file (e.g. ProRes 422 codec).  There's a free version and a paid version - both will do what you need:
http://www.divergentmedia.com/clipwrap

Handbrake will also do this, I believe:
http://allmybrain.com/2010/01/05/handbrake-can-convert-mts-files-for-mac/