I'm in a Social PhD program (1st year), and I have a MA in Psychology from a different college.
I think each university (and maybe even each program within each department) may treat things differently. For me, it's a bit complicated. First, they won't "officially" look at my transcript for the purposes of transferring credits until one year is completed. Second, the credits themselves are looked at separately from the MA thesis. The thesis can be accepted or rejected independent of the other credits. If the thesis is accepted, the thesis requirement gets waived, and some mandatory research credits get credited to me.
For the transfer of class credits, they can either a) waive me out of some required courses, where others must be substituted; b) actually take the place of the required courses (shaving some credits of my minimum to graduate); or c) fall into some electives, fulfilling some distribution requirements and taking some credits off my required total.
My MA was 45 credits. With the classes I've already taken this year, my expectation is that I'll take at least 4 classes off my list (the equivalent of a year of classes). I have been told that my masters thesis should be accepted, since it was empirical. That would be another year off of my total (mainly research credits). So technically speaking, if all goes as planned, I'd skip being a 2nd or 3rd year, and jump right into 4th year status.
One issue is that some programs (including mine) will only guarantee funding for a certain number of years. If you have an accepted MA, you go from 5 years guaranteed funding to 3 years guaranteed funding. Meaning I'd have a hardcore 2 years to look forward to.
All that being said, I would absolutely not recommend doing an MA with the idea of transferring credits to a PhD. The only reason I got my MA is because I was in a combined BA/MA program. MA programs typically don't fund students... it will be a big expense with potentially no real benefit. Unless your GPA was low, you're better off improving your GREs, getting more research experience, and revising your goals/statements of purpose.
Hope this helps!