No, you cannot bookmark on Flipside. Here is the response for there tech support:
From: Haemish Graham ([email protected])
Sent: Fri, 21 Dec 2007 23:51:51 +0000
Subject: Re: FlipSide Feedback
Hi.
There are currently no bookmarking capabilities, although you can seek
in a track by holding down [Alt] or [Shift] and moving the trackball.
You can copy podcasts to your storage card and listen to them with
FlipSide, I regularly listen to podcasts using FlipSide.