Name the ips file as the same name as the rom with the exception of of the extension and place it in the same directory as the rom and make sure that Options>Emulator>Automatic IPS Patching is enabled in the VBA. You can also use an ips patcher to permanently patch it for you. Here is the one that I use:
GBATA
http://www.gbadat.altervista.org/tools.htm