Generally, I just try to vacuum around them gently.

I dig a hole nearby in the gravel, and then keeping the vac end down on the glass bottom of the tank, slowly move it around the root area.

I don't worry if I don't get all the gunk because every 6 months or so, I gently pull up my plants, vacuum thououghly, and replace them.

I have this need to rearrange my tanks' designs about that often.

I agree with Angelee about getting some type of reference book on plants. I'm planning on picking one up soon so I can rearrange with some new flora, and learn more about the benefits/expenses involved in potting your own plants.