The fountain covers the standard bases, but the bottled lineup is where it gets more specific.
Self-serve PepsiCo lineup. Some locations run specialty fountain flavors, an agave vanilla cream soda shows up often enough to be worth trying if your store has it.
PepsiCo's craft soda brand, sold bottled. A step up from a standard can if you want something less mainstream.
Bottled iced tea, flavor selection depends on what that specific store stocks.
Standard bottled options at essentially every location.
Fountain drinks come in two sizes at most locations, 22oz and 32oz, and both show up specifically in the official combo pricing (paired with chips or a cookie at a bundled rate). There isn't a smaller "kid-size" fountain option the way some chains offer, if you're ordering for a child, the 22oz is the standard starting point. Store-to-store, the exact cup sizing can vary slightly since it comes down to what dispenser equipment that location has, but 22oz and 32oz are the two sizes referenced consistently enough to treat as the standard.
The official menu lists several drink-and-chips bundles directly: a 20oz bottled drink with chips, Pure Leaf Tea with chips, and both 22oz and 32oz fountain sizes paired with chips. Each of these runs cheaper than buying the drink and the chips as two separate items, worth using anytime you know you want both.
No strict pairing rule here, but water or unsweetened tea is the straightforward choice if you're also trying to keep the meal lighter, since a fountain soda adds real sugar on top of the sub itself. If you're going for the full combo experience, the drink-and-chips bundles above are built for exactly that, and pairing works with either a cold sub or a hot sub equally well, there's no drink that specifically clashes with one or the other.