I have a 55g community with the middle gravel and sand around it up to the edge of the tank. I'm using a filter rated for a 75 gallon aquarium I want to keep the bottom very clean without intermingling the two different kinds to much.
I would use a smaller siphon than you might normally on a tank that size, especially when you are working next to the border. Go really slow, and do not allow the siphon to cross the line or pick up both materials at one time.
Also, minimize the amount of actual substrate disturbance. Allow the roots to get well established and hold the materials in place. Sand and gravel are not the best for this, roots seem to prefer finer materials, but it will help.