Hi @wildbill,
I saw your question on Discord and was just about to answer you there, but this is a good place for the answer so others can find it quickly.
If you want to use a custom version of a module or a system, you can always import it via the Import Wizard.
Do note however, that since it’s a custom version, you would need to change the version of the system/module in the system.json/module.json file of the package (from 0.2 to 0.2-custom or 0.2.1-beta for example). It is after all a different version so you need to reflect that 
If the name and version of the package matches one in the Bazaar, it will use the Bazaar version of the package when it installs it, but if it’s a custom version, it will import your custom package. Note however that if you do a ‘check for updates’, it will always suggest an update to the package.
I hope that helps.