I know this may seem obvious to many, but I have had trouble going up into pipes when I've used the Propeller Jump. Does using that move prevent you from going into a pipe, or am I simply not aiming well enough?
Yes, you can, and there are at least a few pipes that are really only accessible in this way, particularly in single player. Here's a video example of one such pipe (Note: this does contain something of an exploration spoiler):
As I recall, you can simply hold the up button as you propel yourself upwards, so I would suggest trying that. That was typically pretty consistent for me.