Because the Miniak does not offer a way for external editors to fetch the current edit buffer on the synth (without knowing which patch is being edited), Patch Base uses a workaround: Patch Base designates 1 slot on your synth's memory as a sort of "scratch pad" where it stores the patch you're working on. By default this is slot 127 in bank 7 on the synth, but you can change this to whatever you'd like in the "Global" tab/window of Patch Base. Just be careful not to set this "Write" location to a location that stores a program you want to keep safe.
While this approach is a bit "weird", it also gets around a couple of limitations that almost all Miniak editors in the past faced: with Patch Base, you can add additional "Mods" to your patch via the editor, without adding them on the synth first. Also, you can change the name of a patch from the editor as well.
Similarly, Patch Base has a "Fetch" location setting (also in "Global") that determines which Program will be fetched from the synth when you tap the Fetch button in Patch Base; generally, you don't need to set this manually; Patch Base will listen to messages from the synth to know which Program is currently being played, and should keep things in sync for you so that you can just tap the "Fetch" button whenever you want to start editing the current selected sound.
The Miniak has a non-traditional structure to its Program Banks; some parts of a Bank can be "empty" rather than having a patch in them. In order for this structure to work with Patch Base, a small workaround has to be used. To Fetch Program Banks from your synth into Patch Base:
Patch Base manages Programs on your synth according to their Bank/Patch location on the synth. When you scroll through sounds on the Miniak itself, they are presented in alphabetical order; not the order they are stored in the banks. If you ever want to know the Bank/Patch location of a sound you're playing on the synth, just press and hold the "Programs" button on the synth, and it will be displayed on the screen.