I have a ton of user waypoints around my home base for places that I like to land off airport. The problem is when I got back to my flight log it only uses the closest airport in the database as the destination. So they either show up as me going to some airport 20 miles away I didn't goto or Lcl flights. Is there someplace in the menu where I can tell it use my my user waypoints? Would sure make it easier when filling in my log book after a day of hopping all over to different places. I'm using a 396 I guess that's worth mentioning.

You have the 396, right?

On my 396 in Aviation mode. I press the "Nearest" bottom. Then scroll over the the "User" section and all of my user inputted way-points are listed.

I hope this kind of helps.

Edit:
Never mind. I had my head up where the sun don't shine I just reread your OP and realized the second time your talking about something different

I use the iPad with foreflight and logtenpro. User waypoints show up automatically (name or gps coords) when I send a flight from the file&brief section of foreflight to logtenpro.