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.
6. Open "Clover.gba" in your emulator.
7. Play!