Welcome! If you are totally new to MS, my advice is just be aware that it can seem overwhelming, but remember it is by no means impossible to understand, and just take it in little chunks at a time. Feel free to open up a new thread and I'll answer as much as I can.
The exact answer on how to hook VVT up depends on a lot of factors, so there is not a simple answer really. It depends on what other input/outputs are already in use and for what. Here is the relevant megasquirt doc:
The DIY autotune article is probably easier to read, so give that a look as well:
The gist of it is that have to find an unused output pin on the CPU, set up a transistor to step up the amperage, and then either have the transistor activate a relay wired to activate the vvt solenoid, or depending on how much the transistor steps up amps it might be used to power the vvt solenoid directly.
For all I know, the guy who build your MS already set up something for this purpose and you just have to find it.
The circuit to build in the ECU in the prototyping area to run the relay uses these parts:
Then it's just a wire from the coil side of the relay to the ECU, +12v wire to the coil side of the relay, another +12v wire to the vvt solenoid, a wire from the other pin on the solenoid to the switched side of the relay, and a wire from the other side of switched site to ground.
As to the pros/cons, I don't have the dyno time under my belt to speak from authority, but the general consensus among forum warriors seems to be that VVT can improve [mid, top) range power, at least if using stock internals and piping.
Don't worry about which sensors are not being used, just look in tuner studio and make sure it is getting a signal for each major thing. IE, make sure it has an air intake reading, water temp reading, etc. It may have been set up with non-stock sensors so the original sensors may be unused.