Technically speaking, you are kinda screwed. The real way to get around it would be to have "custom" lineups set at the beginning of the season (or at least sometime before your big guns might get injured), and call up those lineups.

As far as getting around it for this week, here's my best guess :
Activate a player that you do not intend to have on your active roster this week. Stick him in the catcher slot, where you want Pudge to hit. After you set this lineup, deactivate that player, thus leaving a blank, where the ROBOT will presumably put the best available player for that position.
Of course, to do this, you need to have your rotation set up properly, because you won't be able to specify your starter for those games you want Pudge to play in.
You can obviously set up a "custom" lineup for the first 3 games of the week, with whatever catcher you want......

Funny you ask that this week, as I have the same situation, though it's only with Mark Loretta, so it's certainly not as big a deal....

Unless you or someone else smarter than me comes up with an actual solution, let me know if this works...