I like modeling my joinery right over the top of my timber components. I work outside of the 'container' - and just draw on the ends of timbers. When the joinery is complete (without pegs) - I create the component.
To get the TFJoint exactly back in its proper place I Edit>Cut the component, open the timber components, and then use Edit>Paste in Place.
This is especially helpful when working on compound joinery, as I've found lining up things with odd angles in the midst of complex models can be tricky. To do this I usually make a copy of the component I want to add joinery to and drag it over to the side. I'll draw on the joinery, create the component, and then 'copy' and 'paste in place'.
After getting it inside the timber component I'll then 'TF Create Joint' and add pegs as needed.
I've found this method to simplify things... especially when teaching someone new to SketchUp and TF. It solves some of the problems of being sure to only select specific faces / lines while inside a complicated timber.
