I also intend on printing my comic! My original files are MASSIVE, and I put everything together for my standard pages in Clip Studio Paint. Below is an example of one of my original pages in the program:
The way my files are set up, each panel is clipped within it's own folder. It's really simple for me to hide the layers for the black borders, and either save each panel as an individual image or just with transparency as below.
I also save out images for things like sound effects and speech bubbles, which I individually resize along with the panels when assembling the endless scroll version.
You might be able to accomplish something similar in other programs, but I'm not exactly sure. I'd be happy to answer other questions, though!