It's not second nature, or even close, but I found that as you do more nav trips it gets much better - hang in there
The first few I did were a nightmare of paper-juggling, wrestling the aeroplane for height and heading and constantly being reminded that I hadn't checked the DI or that I hadn't set the comm box for the next radio call (which I needed to make in the next 17 seconds before I wandered into the Farnborough MATZ). Gradually things got easier, and by the time I did my QXC I was spending most of the time looking out of the window - I knew where I was, height & heading OK, checks done, comm box set and 5 minutes to run to the next waypoint.
Tips? Fly height (trim!) and heading, of course, but also don't put waypoints too close together because there's extra work to be done at each one. I started off with waypoints less than 10 miles apart but now use one every 20 miles or so - even if I fly the leg 10 degrees off track I'll only be 3 miles from the waypoint. At each waypoint do whatever you are taught - mine was Turn, Time, Talk (& Set if required) and your checks - and then you're done until the next waypoint. Look out of the window for other traffic, and enjoy