I would like to know this too. It should be possible to manually mark a subscription as paid right?

It should, but there is add external payments or mark an invoice as paid.

Since we have multiple external payment methods this is how we do it:

• Setup for each subscription type (e.g. premium, vip etc. however you have divided your plans)
  • A Free Plan (All Amounts 0)
  • With Frequency "No Auto Recursion (custom)".
  • Disable it so it wont show up on the hosted pages (Active = unchecked)
• When a customer pays through an external source
  • Find or create the customer
  • Click the "Edit Pricing Plan" button
    • Choose the newly created free plan of the chosen plan type (in the drop down you can find the deactivated plans as well!)
    • Set the validity accordingly
  • IMPORANT: Now cancel the subscription right away!
    Otherwise when the subscription runs out the subscription is in an undefined state since the system doesn't know what to-do (since the plan is not auto recurring)

We are using this procedure with multiple external payment methods and it's working fairly well, we have even automated this process for our most used external payment method (moneybookers).