As for your tempo changes, record first with a metronome set to different BPMs for each part and add the instant drummer parts later. Somtimes a break with just bass and drums, no drums or a sustaining chord ringing out helps the transition between time changes go smoother.
One approach that may help your transitions between riffs is to record with another pre-recorded riff as the "lead in". Instead of using the metronome or drummer part as a lead in before you record, have RiffWorks use one of the riffs you've already recorded. Then it will record to BOTH riffs as separate layers. When you place these riffs side by side on the time line the transition will be smoother.
From the RiffWorks manual:
Riff As Lead-In
"Under the LEAD IN section of the Riff Recorder, you have the option of selecting any one of your Riffs as a LEAD IN. When you select a Riff as a LEAD IN, you will be able to record a layer on that Riff before that Riff Recorder switches over to your current active Riff. This is very useful if you want to record a few pickup notes from one section to another. It will make your transitions much more seamless."
Also, learn about and experiment with song layers:
http://www.sonomawireworks.com/guide/index.php/SongLayersAlso, here's a good tip from Pooter on transitions: Add some *slight* delay or reverb in Riffworks to your lead Layer. This will help the end of one riff "bleed" into the next just a little, making things a little more seamless. If you add delay or reverb on your tone patches you won't get the same effect.