I'll quote myself here:
I've recently converted to Affinity Photo for my graphics software and it's killer. A bit of a learning curve if you're not used to working with layers but it's ability to pull in individual sheets from a PDF is a cool trick. So if the box layout is, say, page 6 of the build doc: open the PDF in Affinity, specify Page 6, import at 300dpi to keep the edges sharp, and then save it as the Affinity file format. Make sure you print at 100% and you don't have to worry about getting the size right.
From there just add text, frames, artwork, or whatever strikes your fancy. You can set opacity (transparency) on a per layer basis so lining up text with the holes is a breeze. When you print to the decal, turn off the background layer you used to line everything up, turn opacity back to 100% (unless you're using it as an effect) and let rip thru the printer.