Paying extra for a 3d movie with MP should have nothing to do with the theater. What is supposed to eventually happen should be fully transparent to the theater as it is now when it is fully implemented on MP according to an email recently received. You should be able to buy the ticket to the 3-D and they (MP) will charge an extra fee to your credit card that is on file with them when you signed up. As far as the theater is concerned MP should be no different than paying with your debit card, You say "3D" they take the card and the 3D difference will be charged to your CC on file through MP.
Thing is, this is not fully implemented yet nationwide, it's still being tested. Doubt it is available here. If it is, someone needs to tell the cashiers at our theaters. You will also be able to bring others (non-members) using your card and pay for it the same way as the "3D fee." This avoids all the separate payments for friends and family. MP is simply a pre-loaded debit card to the cashier. The cashiers think they know the rules but hopefully they will eventually be instructed to simply take the card when it is all implemented.
Also (if you read their "fine print" T&C) it seems that you can use their cards loaded funds anywhere but if you get caught they will cancel you (it's just a Master-Debit card) . All you do is "sign-in" to a movie which puts the funds on the MP card then go to any other store and spend the money that they pre-loaded for the tickets. I've read of people who have done that and got dropped. Their T&C seems to say it is possible.
Also, for those with yearly passes (ex. Costco) the new rules that are already implemented (1 movie per day and/or can't see the same film twice and probably "surge pricing") do not apply until end of your current year.
And finally, keep your fingers crossed that they are still around by the end of the year. They are having all kinds of financial problems due to the very low cost. Just Google them.
As for the outage of last week, you can read about it here:
MoviePass says it will refund users who were affected by last night’s outage - The Verge