With 5/3/1 you obviously should do the main movement as a standalone, to respect the intent of the program. Work done to learn to "feel" the muscle should be thus done as assistance work.
You don't always program all the small part of a muscle before doing a compound lift. For example you wont necessarily be able to feel the lateral portion of the deltoid doing the work on a shoulder press. But you should feel it in the overall shoulders.
But you can still do an isolation exercise for the lateral portion of the deltoid. For example you could do a set of lateral raises right before (superset) doing a set of dumbbell shoulder press.
For the lateral raise you should focus on pushing the arms away to your sides instead of thinking about lifting them up. You should also use a constant tension repetition style: never relaxing the muscles during a set. That means not going all the way down and holding the weight 1 second at the top focusing on contracting the deltoids.
For the rear deltoid you can activate it with the rear delts machine (reverse pec deck) with a pronated grip done in the same rep style as above, then immediately doing a set of seated cable row (or barbell row) where you pull toward your chest.