When I'm scheduling myself, I build in time to do the reports in my daily schedule. I do, sometimes, use my phone to upload photos to my reports or answer short questions, but I find that trying to write anything detailed is difficult on the phone, so I wait to do that when I get home. I also complete my reports in the order that they are due, as opposed to the order that I did the shop. Since some reports must be completed in 12 hours, some by midnight the same day, some within 24 hours, and so on, I know which ones I have a little more room to "put off" than others.
Also, when I'm scheduling shops, I have a pretty good idea of which ones are going to be simple multiple choice and which will need more detailed narratives. Then, I try to not book myself with a day full of long, complicated reports to write. As you do them, this will be second nature to you too, I'm sure.
I keep a day-planner, where I list every shop I have to do that day, along with the MSC I'm doing the shop for. Then, I make a check-mark when the shop is done and another when the report is done. This way I know what needs to be completed and which reports I have left.
The trick is really to be organized in whatever way works for you and systematically knock them out.
Good Luck!