I recently did a full substrate swap on my 10g w/o an issue. The biggest thing you need to look out for is losing too much of the bacteria at once. I did this with regular gravel, so it may be useless with a muddy type of substrate on the bottom. First I would say put some prefilters on your filters to keep the muddy stuff out of them. With my swap, I never had a detecable spike of ammonia or nitrites aftwewards. Here is how I did it:
1.) Everytime you do a water change for a few weeks, remove some of the substrate. Try to get about 20% of the substrate out at a time. Once you get to about 1/4 inch to 1/2 inch of substrate across the tank you will be OK. This process causes the bacteria to find other places to live.
2.) Let the filters get full of bacteria-filled waste. Mature filter material is crucial for good bio filtration and also help with the mechanical filtration as well. You can start building up gunk in the filter once you start removing substrate.
3.) Once you are ready to make the switch, vacuum the gravel in the whole tank to remove as much waste as possible. Taking out about 40% of the water will be good, do not replace the water yet.
4.) Place all tank plants and ornaments in the old tank water.
5.) Scoop out substrate with a net/hand/whatever, once you get the substrate up off the bottom, shake the net around, some waste will come out (do not do with sand/mud). Once you get it out of the water, let it drip into the tank for a few seconds. The tank will turn into a cloudy mess at this point, but keep moving forward. Keep and eye out for stupid fish during this time. With the mature filter material in both of my filters, the tank cleared up pretty nicely in about an hour. Having less water in the tank helps for this step too, as your filters can cycle through the tank water faster, and you do not have to worry about spilling water out of the tank or anything.
6.) Once the tank is cleared up, add new substrate in small ammounts. Put the new substrate in a net, lower it into the tank, and dump it so no fish get in the way.
7.) Refill tank with treated water.
8.) Re-add plants/decorations.
9.) Your fish will likely be stressed at this point from all the commotion, so just turn off the tank light and put them to sleep for the day.