There is no requirement for how you organize or number your PQR's. Only that you address the required variables.
I do split as welded's and PWHT's all the time, or, I used to. Organize however is most convenient for you. Also consider making it easy to understand by your customers who will review your procedures and will almost always be very confused.

Each welding document, i.e., PQRs and WPSs, should have a unique identification assigned to it.

Any system is acceptable. You can give the PQRs boy's names; Sam, Willie, or Butch, and you can give the WPSs girl's names: Sallie, Sue, Greta, Judy, etc. You can use numbers that are consecutive or an alphanumeric system can be used.

I like to be able to look at the unique designation and know what the welding document contains. All my PQR start with the letters PQR. All my WPSs start with the letters WPS. It took years to figure that out.

Next I assign a letter or two for the welding process; GTAW - GTA, GMAW - GMA, SMAW - SMA, again years of effort went into this before it was finalized.

Then I designate the base metals to be welded. I use P or M numbers for this. It is easy to remember since I write WPSs on a daily basis (well almost on a daily basis); P/M-1 for Carbon Steel, P/M-8 for austentic stainless steel, P/M-for heat treatable 6061 or 6063 aluminum, etc.

The filler metal used is defined by the F number; F4 for low hydrogen SMAW electrode, F6 for carbon steel filler metal used with FCAW, GMAW, or GTAW, F23 for ER4043 used to weld aluminum, etc.

Lastly, if needed, I add a discriminator, i.e., the lower case letters a, b, c, etc.

So an example might look like this:  WPS: GTA-1/8/F6a. I now know that I am using GTAW to weld carbon steel to austenitic stainless steel using an F6 filler metal. The discrinator "a" may differentiate this procedure that uses argon shielding gas from another procedure that uses a inert mix of argon and helium (on steel?) or a procedure that is intended for open root joints in tubular structures versus nontubular joints made with backing. The exact nature of the difference is determined when the WPS is reviewed, but at least I know it is different from WPS: GTA-1/8/F6b.

The system can be expanded or contracted as the need arises. For eacmple: WPS: GTA-1F6 would be for GTAW of carbon steel using an F6 filler metal. The designation provides me with enough information I know whether it is applicable to my work or that I need to keep looking for one that better suits my needs.

My objection to a simple numeric system where consecutive numbers are used is that it is too hard to locate and select the appropriate procedure when the company has more than one or two procedures. I worked with one client that had a notebook containing over 300 different procedures starting with 001 ending with 324. You had to look through each procedure until you stumbled across the one that was applicable to the work that needed to be done.

Any system will work, but settle on one that has some rational to it.

In your case I would use something like PQR: SMA-1F4a and PQR: SMA-1F4b, one being "as welded" and the other "with PWHT". They are really two separate PQRs because one is "as welded" and the with "PWHT' which is an essential variable. In other words, if the procedure was initially qualified without PWHT, i.e., "as welded" and then you decided to perform PWHT, you would have to requalify the procedure by welding and testing another test plate. You would have two separate PQRs. You are essentially doing the same thing, except you are welding one plate and spliting it. You still have two separate PQRs because each piece is subjected to a separate battery of tests and they are reported independently of each other. The only time I would combine the PQRs is if it was a case of "all pass or all fail." That isn't what you are doing, one set can be acceptable, either the "as welded" or the "PWHT", while the other can fail. You would only weld a separate test plate and retest it to qualify the one set that initially failed to meet the mechanical properties.

The two separate PQRs can be used to support one WPS that includes both "as welded" and "PWHT" conditions.

Best regard - Al