Have been using a Lowrance Outboard Autopilot in conjunction with my HDS Gen 2 Touch 9 for three seasons with great success (as you know, the HDS 2 is similar to your HDS 3).
Have trolled thousands of hours after salmonids and char on the great lakes with no complaints on this AP and the sonar unit. Here are some tips from a previous C Brats post from a while back:
http://www.c-brats.com/viewtopic.php?p= ... 3c2a550814
As far as I am concerned, this AP is the best only because it does one thing very well that some of the other AP's do not: it works well with the sonar unit at SLOW trolling speeds (<1 mile per hour) . Also, you have a myriad of features that some of the other AP's typically used don't have. My favorite? The zig zag feature within the "patterns" sub setting that allows you to set your stern to move back and forth in the water (without losing your course), thus activating your down rigger sets to rise/fall and speed up/slow down. On calm days, this is a game changer and gets you strikes that would have never happened.
You can control this AP right from the screen of your HDS 3 by adding a third window to your display, no additional visible hardware is needed on your helm. The GPS antennae is mounted on your roof, and the NAC 1 computer is installed somewhere under your helm or under your seat.
I could go on, but read the in's and out's of the topic I listed above and you'll an earful.
Good luck, and PM me if you have any specific questions or want to talk over the phone.
Cheers,
D