1. First off... you have a Marshall 4x12 and a Mesa 2x12. I'll assume it's the Marshall 1960, which is 16 ohm mono or 8-ohm stereo. The Mesa cab is 8-ohm mono.
With your Roadster amp, if you want to use both cabinets, you will be running each cabinet in mono.
As a result, for proper matching of the cabinets to this head, you actually have to connect the 2x12 8-ohm cabinet to a 4-ohm connector, and the 4x12 16-ohm cabinet to an 8-ohm output. This is actually illustrated in your Mesa/Boogie documentation and is the propper mismatch that works most efficiently with your amp.
2. Note that your setup is not at all like John Petrucci's. He is using the Road King, and the speaker connections are one of the fundamental differences between the Road King and its baby brother, the Roadster.
The Road King amps feature Cabinet Switching. In this amp, the 4x12 speaker cabinet would be connected to the 16-ohm output for Speaker A and the 2x12 would be connected to the 8-ohm output for Speaker B.
On each of the four Road King channels, a user selects whether output is sent to Speaker A, Speaker B, or Speaker A+B. This way, on one channel, you may like the sound of a 4x12 closed-back cabinet while on another, you prefer the vintage sound of a 1x12 open-back, for example.
All speaker outputs in the Roadster are effectively one output -- there is no cabinet switching option and thus you have to deal with speaker impedence mismatches such as with your two cabinets.
I hope this helped clarify things.
Scott
p.s. We'll talk about the few differences between the Roadster and the Road King in our review of the RK Series II amp publishing Sept. 1 at MusicPlayers.com.