I want to highlight parts of the prayers where the congregation responds and where the chazzan speaks so I can better follow the service, as well as write in some notes about the prayer order, etc. Can I write in the siddur or will my rabbi have a meltdown? =)
While I've never done this myself, I don't see any issue with it, provided that you highlight and underline respectfully.
From that blog post:
It's a way to corral ourselves during our distracted moments, and draw ourselves back.
It's a way to personalize our davening, by highlighting elements that matter to us.
It's a way to remember the items that catch our eye or ear and inspire us once, for the next time we daven.
So it seems that it's not just something that you may do, but rather a recommended practice. I wish you much success in focusing on your prayers!
My answer is based on logical deduction.
Many siddurim already include typed English instructions and translations, etc. interspersed between the Hebrew prayers. I don't see the difference whether the publisher has typed instructions or whether you highlight or write your own instructions to help you out.
Provided you're not erasing G-d's name, there should be no problem.