Your WPS is your guiding document.  But, what code are you working to? 

It is entirely possible that it would be acceptable to write a new WPS and get the procedure approved by the engineer on the job and then you could do so. 

If you are working to API 1104 or ASME and have a PQR qualifying your procedure then you may have to get another one prior to writing the new WPS.  All depends upon how the original one was written, tested, and approved in order to establish your procedure. 

There are many aspects of this that you have not given us details for so this is just my two tin pennies worth of free opinion and thoughts on how one might proceed. 

He Is In Control, Have a Great Day,  Brent

If you are working within the scope of ASME Sec IX and most of the B31 codes, using two different WPS's on a single joint is allowed. Even if they are two different processes.

Though it's allowed does not mean it's a good idea. Welding over a ground exx10 root pass with GTAW might not be advised.
These types of questions are best answered by project requirements.

As far as my experience goes, a WPS has to be followed completely. So if it says Fill passes are with SMAW, you have to do it with SMAW.

If you're talking about ASME IX your PQR may, however, be something like GTAW+SMAW, or you might have a GTAW PQR that is accepted /approved by the customer, and in that scenario, you may create a WPS that has RootProcess+GTAW. Please look towards ASME QW 200 (.4 I think) on how to do this.