Well, I may offer some help here. Graphite 49 is an awesome piece of kit for the price, with aftertouch, at more than $100 lower than the next lowest aftertouch, but it's woefully underdocumented. I was looking for you geniuses to improve my setup, but let's start by getting you up to where I am.
You should choose Mackie Control, correct, port 5 in, port 2 out is correct. If it suddenly acts wonky, then just delete the setup and do it again. This will give you control, but no ACT. In MIDI devices (Preferences|Midi Devices) you select just Port 2 and graphite 49 out, and port 5 and Graphite 49 in, and the Mackie setup takes port 5, so you use the graphite 49 as the keyboard into your tracks.
For ACT, I edited user 17 and set it up as an ACT midi Controller, and then I get fader and knob action in all my plug ins. Just wish I knew how to upload the graphite setup to you, and how to export the ACT preset (from sonar) and upload that to you too.
Good Luck, respond if any of this is unclear; or foolish!
Darryl