Hi, Paul,
So, for example, you have vertical footage and then horizontal footage all in one continuous clip, but the horizontal portion displays the video on its side. You want to have the horizontal video play the footage right side up but still fill the screen in a horizontal orientation. Correct?
To do that, you would need to do a Modify/Split clip at the in-point and out-point where the orientation changes. Then select the horizontal clip segment and click on the crop icon (the one that looks like intersecting angles) in the tool bar at the top right of your screen. When the crop controls appear you will see two rectangles with rotation arrows. Click on the rectangles to rotate the clip. Repeat the process as you progress through your video.
To avoid any interruption of the sound track caused by splitting the clips and trimming to eliminate the barrel roll effect of the clips turning, you may need to do a Modify/Detach Audio on the entire origina clip, to display the sound track as an audio clip. Or, if you don't mind displaying the video clip actually turning while changing orientation, then you wouldn't need to detach the audio.
Hope I've understood you correctly and described it clearly.
-- Rich