usbloadergx doesn't load games in extracted format. you'd have to use Wiiscrubber, TruchaSigner or Wit to replace files in an iso/wbfs file.
Another solution if you are heavily modding and testing your files is Neek (it loads extracted game format), or maybe dolphin ?
with neek+di, extract the game partition to sd:/games/TitleID/
Launch neek+di
use the hidden game menu to mount the game and launch it from disc channel.
you'll have to shutdown the console every time you want to edit the game's content. don't do any hot swapping, you'll corrupt your device's partitions.
Riivolution is another solution, but you need the retail disc (or a compatible modchip).
untested, might not work:
If your mods are already in wbfs or iso format, and you want to play them, then it's easier.
/wbfs/gametitle [TitleID6]/TitleID6.wbfs
replace the titleID6 with something else than the original ID (not SMNP01 for example), and the loader will list the game as another game.
if your internal TitleID is not modified, it will use the same savegame than the official game.
it's possible the loader doesn't launch the game because expecting TitleID (the one you provide) doesn't match the one located in the game's header.