Hi Derreck -- This all depends on the pricing plan's configuration. On the pricing plan's Edit page, you can see "Paying Customers Transitioning to this Plan" near the bottom of the form. Here you can select either

1. bill new amount on next billing date
   or
   
2. bill immediately for a prorated amount and start new billing period

Option #1 will not will not prorate.

If a subscriber is on a monthly plan for let's say $6.99/month and decides to upgrade in the middle of the billing cycle to a $12.99/month plan then are the charged the difference at the time of the upgrade?

Yes if option #2.

Or do they get charged the full $12.99 at the next billing period?

Yes if option #1.

What if a user goes from a monthly plan to a quarterly plan? When do they get billed the difference?

Works the same for all frequency types.

It can get a bit tricky, so we have some additional documentation that spells everything out nicely.

Thanks!