This question is more connected to the Silverlight navigation framework, no to the TransitionControl - it is just a content control that shows an animation when its content is changed.
For the navigation framework it doesn't matter where the link buttons are - inside or outside the page, so you can add your buttons wherever you want to.
About the parameters - you could use # and additional parameters in your URI in order to pass parameters. You could refer to the following blog post for more information: http://silverlightedweb.blogspot.com/2009/03/silverlight-3-beta-deep-linking-using.html.
Hope this helps!
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