What you are supposed to do depends on how you are going to tune the car.
If you are going to scale the MAF and not touch the VE table, then no you don't disable the MAF.
If you are going to leave the MAF alone and adjust the VE, then yes you do, but don't get the car into boost.
If you need more help try the search function first (not being a smartass) but I have personally typed up a "starters" tuning post on more than one occasion. There are also some very helpful posts on HP Tuners forum for the VE table (speed density)
If you want to try the MAF scaling method go here:
http://ls1edit.slowcar.net/tuning.html
The author wrote this with LS1 Edit in mind, but it is directly applicable to HP Tuners or whatever you are using.
If you need more help, let me know.