This will put your patched DOL in the folder ./BUILD/ as is described in the README.md. This leaves your original clean DOL file where it still was, in the current directory. This means you can keep patching using the same DOL file with ease.
As for an already patched DOL, the effects will vary. This is designed to find usable sections, so an already patched DOL like one from WSTRT is not an issue. The problem lies in the fact that this will inherently disable mods like LE-CODE, or CT-CODE, since they also hijack the main.dol in a similar manner as this. But this is a MKW specific issue, and not an across the board thing.
Lastly, if you have certain values changed in the main.dol, like instruction swaps, this is fine for GeckoLoader.
As for an already patched DOL, the effects will vary. This is designed to find usable sections, so an already patched DOL like one from WSTRT is not an issue. The problem lies in the fact that this will inherently disable mods like LE-CODE, or CT-CODE, since they also hijack the main.dol in a similar manner as this. But this is a MKW specific issue, and not an across the board thing.
Lastly, if you have certain values changed in the main.dol, like instruction swaps, this is fine for GeckoLoader.
Super Mario Eclipse, what Super Mario Sunshine could've been.