You use Pod HD300 Edit to overwrite/replace existing presets with the ones you have downloaded from Customtone.  The set of factory presets in the HD300 includes some in Bank 32 with the name 'User Preset' or 'New Tone' or something like that. These are the ones to overwrite first, and experiment with, until you get comfortable editing and creating your own set of presets.

My preferred approach when downloading the files is to Save them to a folder on my computer, rather than using the 'Open with...' option in the download dialog box. Once you have them as files on your computer you can simply drag/drop them into the desired preset slot in HD300 Edit. I have found that using the 'Open with...'  tends to always load them into preset slot 1A, which is generally not where I want them, and immediately overwrites the existing preset 1A.

The  Pod HD500/Desktop/Pro support the concept of 'setlists' where you have 8 sets of 64 presets organized in 16 banks of 4, rather than the HD300/400 approach of having a single set of 128 presets organized in 32 banks of 4.