Hi Liam, from your description above, I suppose you are talking about the multitasking feature of iPad Pro, where you can display two apps side by side on the screen. In this case, QuickCapture should work with no problem. If you can provide a screenshot or a short video of the issue (to quickcapture@esri.com), that will help us identify the problem.
Have you also tried the side by side view inside of QuickCapture? You can display your project and the map side by side if you open the QuickCapture project on your iPad in landscape mode. Read about this blog if you are interested, your project will look like this in side by side view: