Not sure what you mean by "mark it for deleting". You delete it, plain and simple.
My preferred method is to un-tick the Podcast in iTunes. This will remove the episode at Sync time. Then I simply delete from iTunes. However, there are a couple of things you need to know.
- Syncs with my iPod Touch have been known to complete without the updating of Podcasts being actioned. Sync a second time.
- If you un-tick, delete, or whatever you do while the iPod is connected to iTunes, your changes nay not be actioned if the Sync process has gone past the Sync-that-stage position. Make the chnages in iTunes before connecting the iPod to it.