The popsloader is if you want to use a different version of the official PS1 emulator. For instance, if you're at M33 3.52-2, you use the 3.52 popsloader by default, with all the fixes Sony has made for the official 3.52 firmware. Some games, however, work better on certain firmwares. That's what the popsloader is for. So if you don't use the PS1 emulator, or if all games work perfectly for you, you don't have to bother with this.
If you do want to try it out, you'll need to decrypt the whole firmware update file of the firmware you want the pops files from, then find the necessary files (which you mentioned earlier). Do this for all the firmwares you want to install the popsloader for, and rename the files accordingly.
Update: No, if you don't want to use the popsloader (you can still use the pops that comes with 3.52), you don't have to do anything more after patching to 3.52-2.