You need to use 2 folders one with the MTS files and the other with the avi copies, then when you have done your edit on the avi files just rename the folder with the MTS file to that of the avi files and just rename the folder with the avi files to something else so the ppj cant find the files and it will ask you were the files are, then you point it to the MTS files, you will probably have to do it for all the files. be aware that if you do any color correction it will slow the encoding down to a snails pace.
If you want a program that will do it for you automaticly check out Corel ProX2, they call it Smart Proxy, you set the resolution of the proxy files to anything that suits the speed of your processor. when you export (Share) the video it automatically selects the MTS files. it makes excellent HD videos but is not as good as Premiere at making DVD mpeg2 files.