Please note that extended RAM games don't work on o3DS/2DS.
But you want to put the cheat files (<filename>.plg) into a folders in a syntax similar to this:
SD:\plugin\<title id>\filename.plg
So, for example if you wanted to use my Animal Crossing plugin, download it and your SD card should look like this
SD:\plugin\0004000000086400\ACNL_CHEATS_EUR.plg (assuming you're using the europe version of Animal Crossing.
Usually most devs zip their plugin so that it's easy to just drag and drop the title ID folder into the plugin folder, but if you just get the .plg, you can simply look up the Title ID of your game
here and then make the folder manually
Also, some cheats have different menus. Gateshark2ntr plugins, which are the most common, are called on by pressing select to open the menu so you can select your cheats. If they're not from Gateshark2ntr, then there'll be a sub menu when you press 'X + Y' called 'game plugin'
All of the plugins I made use Gateshark2ntr's library, so you have to press select to open the menu.
Hope this helps