How to update Clover step by step for dummies:

For each update, you need to apply the updated .ips to a CLEAN ROM of Firered.
If you apply it to the ROM you're currently playing on, there would be game-breaking glitches. Trust me, I've seen it.
Make sure your Emulator is turned off before doing this:

0. Download the "Clover.ips" from https://goo.gl/ofQBSK
1. Find and download "1636 - Pokemon Firered (U)(Squirrels)" (search for it on Google).
2. Apply the "Clover.ips" to the newly downloaded "1636 - Pokemon Firered (U)(Squirrels)".
3. Copy over your save file (.sav) to the folder your newly patched "1636 - Pokemon Firered (U)(Squirrels)" is in.
4. Rename "1636 - Pokemon Firered (U)(Squirrels)" to "Clover" for simplicity's sake.
5. Rename your save file to "Clover" as well (the save file and rom need to be named the same).
6. Open "Clover.gba" in your emulator.
7. Play!