i had a hard time with this also. i use Eco Complete in most of my planted tanks and just siphon off the top. i also keep Malaysian Trumpet Snails in my tanks to keep the gravel turned around. about once a year i dig up most of my plants and give a really good vacuum, then replant. as a general rule i only vacuum the top 1/2 inch.
anyways, you dont have to use EC (although i find it more convenient) sand/gravel mixture works well (more sand than gravel).
here is (IMHO) the best ever planted freshwater aquarium book, you can find it much cheaper BTW.
Chris- Husband, 04/30/77
Cailyn- Daughter, 07/05/99
Jeffrey- Son, 03/24/06
Alex- Son, 03/25/09
Mister- Black LabX, M, 08/06(?)
The Shadow Stalker- Gray Tux DSH, M, 04/04
The Mighty Hunter- Black Tux DSH, M, 04/04
Baby Girl- Tabby DMH, F, 12/03(?)
Frances- Tortie, DSH, F, 2007(?)