1. Delete the "Mega Power 4.1.gba".
2. Apply the "Mega Power 5.55.ups" to the "1986 - Pokemon Emerald (U)(Trashman)" ROM
3. Copy over your save file (.sav) to the folder your newly patched "1986 - Pokemon Emerald(U)(Trashman)" is in.
4. Rename "1986 - Pokemon Emerald (U)(Trashman)" to "Mega Power 5.55" for simplicity's sake.
5. Rename your save file to "Mega Power 5.55" as well (the save file and rom need to be named the same).
6. Open "Mega Power 5.55" in your emulator.
7. Play!
This is edited from another hack's update instructions and the files may have different names.