Hello,
You may find this thread useful.

Jeroen

The short answer is: you can connect it (physically) to your layout on a siding, the programming track just has to be electrically isolated from the rest of the track. Think of it as a separate electrical zone. Just put track isolators between the programming track and where it physically connects to the rest of the layout. Depending on the track used, the solutions can vary. For C track you have those red caps that you put on the B & O connectors.

Now there is some discussion about the transition, that short time when the loco and slider bridge the two as the loco transitions from the main layout onto the programming track. There are mechanical switches that can be installed to have the "programming" track be just the main layout signal, and when you flip the toggle switch after the loco is in the programming area, then it switches that isolate track section from the main layout signals to the programming signals (and maybe lights up an LED to indicate the status, and if your really want to go to town, closes a physical barrier at the entrance to the programming track just to be really elaborate about it (and fun).