Just to be safe you can verify game files in Steam before installing the HF Patch if you messed with your installation folder before doing this.
It won't hurt anything if you have it installed already, the patch will figure itself out. Special patch is included in HF Patch, you don't have to install it manually. You can remove the downloaded patch installation files now if you want to save some space. The default settings should work well for most users, especially newcomers. zip files from GitHub - they contain source code for the patch, not the patch itself.
You can place these files anywhere you want.
(Optional) Install the AfterParty DLC (or the JP versions).