Really, a the overwhelming majority of proofreading falls back on me. My process is this:

1. Finish the novel.
2. Do a proofing run. I find this works best if I upload it to KDP, download the MOBI file, then use the Kindle emulator.
3. Send it to my editor.
4. Accept the changes in the Word document, and address her comments in order. Revise as necessary. Correct. Address. If it isn't clear in her mind, it isn't clear to the reader. I don't respond. I just make sure that the question raised will not be a question from the reader.
5. Upload the edited version to KDP. This time I send the MOBI to my Kindle device. Which is the Kindle app on my Ipad.
6. Spend the next few days critically reading. I tend to find the most errors when I am drunk in the bar.
7. Rinse, repeat until I cannot find any more errors.

This process has served me well on my last few.