A good idea when using several distortions and overdrives is to put them in order from lowest gain to highest.
With a Valvetronix, you don't even need the effects or the tuner, since they're built into the amp already.
Amplitube does have a pitch shifting pedal like the Whammy, but as far as I know, the only way to control it is using IK's Stomp IO foot controller, which is probably going to be pretty expensive.
I actually record a few different ways. At home when I don't want to go through alot of trouble, I just record direct. Guitar into Presonus Firebox and I'll use VSTs like Guitar Rig 2, Amplitube 2, and Revalver MKII. If I need something a little more organic, I'll use one of my tube heads in the signal. (Guitar > Tube head > THD Hotplate > Firebox > cab sim software) And finally, when only the real thing will do, I'll setup a speaker cab inside my isolation box with a few mics, get everyone out of the house, warn the neighbors, and record at wall-shaking volume.
Do me a favor and check your amp for every input and output and tell me what they are. I'll be able to help a little more knowing exactly what you have.