Worked like a charm!
For anyone in the future that might have a hard time finding the process and need to do the same thing as me, I've decided to record the process-
1. The SNES emulator I used was ZSNESW. The save file I used was called "Chrono Trigger.srm"
2. I copied the save file to the desktop and renamed it "savedata.bin" (I didn't have to byteswap or pad or trim or anything!)
3. I extracted the Virtual Console save file with SaveGame Manager GX to my sd card on the Wii.
4. It gave me a folder with a bunch of letters and numbers in the root of my sd card. Go into that with your computer.
5. Replace "savedata.bin" with the new "savedata.bin" that you put on the desktop.
6. Put the sd card back in, open up SaveGame Manager GX again, go to your sd card. Mine showed a little "Chrono Trigger" icon which was the save file.
7. Click on that and then click on "install." BOOM! Done.
Thanks again!