Currently you can only Mark one Order as Paid at a time. This is extremely cumbersome. I was chatting with support and they even told me it was possible, because the GUI makes it appear so. You are allowed to select all orders on the page and then click the Mark as Paid button, enter your Amount Paid and Shipping Paid info and submit...and you think it's going to work, but then it only Marks the top order in your selection. Such a tease! Boooooo. I'm on my way to go manually mark 75 orders as Paid, so I'll check back here in 30-45 minutes to see if I've gotten any votes. Hopefully I don't fall asleep during this tedious process.
And for the record, check out all the other times this has been suggested and archived(I found these in a 2 minute search, there are likely more):
http://support.shipstation.com/forums/126593-request-a-new-shipstation-feature/suggestions/3058949-m...
http://support.shipstation.com/forums/126593-request-a-new-shipstation-feature/suggestions/6727388-m...
http://support.shipstation.com/forums/126593-request-a-new-shipstation-feature/suggestions/6826953-b...
Can we move all of those votes to this feature request since they are archived?