It's three forms of payment per transaction, regardless of how many people are on that transaction. If you book your daughter and you on the same reservation, you will be able to use 3 payment methods total.
As a related aside, I would not book her on a separate reservation. If you do that, then your reservation won't be 'connected' to hers in the system. If anything happens to your flight, it will make it much harder to deal with because the system doesn't know you're together.
An example: My brother, sister-in-law, niece, nephew, mom and dad, all booked the same flight to Orlando in June. My parents booked separately from the rest of the family, so it's two reservations. SW did some schedule shifting, so the flight they originally booked no longer existed. They moved my parents to another flight on the same day, and moved my brother's family to a different flight (still on the same day). My mom was able to call and get the last two seats so they're all on the same plane. But SW didn't know they were flying together because it was two separate reservations, so when they had to change schedules the system didn't 'know' to move them all together.