Omskie, I think you're confused.
From what I understand, your wife originally arrived on a fiancee visa, and you have since married.
So, all well & good. You've complied with the visa conditions.
Therefore, there's no need for a "spousal visa", nor will they contemplate issuing one.
The next step is the FLR.
If you want her married name to be use, I'd suggest you get yourself along to the Philippine Embassy, register the marriage (which is an obligation on your part anyway), and get them to amend the name in her passport.
This will only take a day. Leave passport in the morning / collect in the afternoon.
Then, when you fill in the FLR application, you can use her married name, (ie, the name in her passport) and use her maiden name in the section where it says "know by previous names".
BTW .... remember, she also needs to do the English test
