Your formation is okay, but it's kinda front loaded. Two Electricity users, and early on you've got some redundancy in the physical department as I'm sure your sub-persons aren't covering all your weaknesses just yet. Zen and Rei are fantastic, but you also likely have no instant kills at your disposal, so that can make dealing with pesky enemies (especially in the back row!) a bit of an issue. Naoto is godlike, and tied with Aigis for the game's best party member. Don't be afraid to use her and have her take out enemies that are troubling you in a fight.
Biggest thing to remember, however, is that this is
not like Persona 3 and Persona 4. You often do not even need to go for the weaknesses. The boost effect is nice (free healing!), but is in no way mandatory, and you can't easily supress turns like you can in the One More! system. Sometimes, using the more powerful skill is a better choice. Physical skills and status effects are very effective here, and you can score critical hits with the former. Especially if you're using members with high luck. Curse and Poison specifically are very strong early on. I don't remember if Zen starts with his physical skill that curses, but try to use it if he has it. Nothing is more awesome than watching your enemies take half the damage they dish out back at you.
I remember early on I was trying to fuse my Sub-Personas like I did in P3 and P4. Trying to cover specific niches in order to account for weaknesses, like a persona with all four elements, a support Persona, a healing Persona, etc.... It wasn't very effective. When I realized this, and instead started building Personas to supplement the party members and their existing skills with less regard to weaknesses, things went a LOT smoother.