I select the piece of track in the middle and it raises everything up instead.
I want the to and from to be a 3% grade with the middle being about 5 inches tall
Please make sure you've read the Editing Track Heights section in the manual that describes the various modes that are available to change the elevation and grade of tracks. Depending on what you're trying to achieve the function that is used and its parameters will vary.
If the question persists please describe the specific steps you've performed so we can provide the best assistance!