I used PDFpenPro ( https://pdfpen.com/pdfpenpro/ ). I was fortunate that the scans I had of the original parts were all pretty straight, and all at about the same scale, so I was able to just select measures from one PDF and drop it into the other PDF, and it usually just worked.
I use red sticky circles. I put them right at the end of the previous sound (so that way if there are rests, it's ready to go). If it's a quick change and I need to incorporate the change of sound on a beat, I'll use a red colored pencil to draw a line above and below the red sticky to indicate the beat. (The red sticky will therefore be on a beat.)
I also use a foot pedal to change my patches instead of one of the keys. This works especially well in fast patch changes because I don't need to move my hands away from the area of the keyboard I'm playing.
The red sticky is good for me because it's bold and colorful on the page so I know I won't miss it. If I marked in pencil or something, it might blend in with the notes or other notations I've made.
Hope this helps! :)