For gravel, (and I'm assuming you're using a siphon here) moving the hose deep into the substrate so it gets the crap *grin* up and out works well for me. Then again, I don't have plants in that tank so I can be pretty thorough.
I also have sand in my planted tank. I use a smaller diameter siphon and just hover the end right above the sand. The detritus sits on the surface, so it comes right up. Also, because sand has less airspace between grains, very little of the deritus sinks in so its not necessary to dig in anyway. A little bit of sand will come along, but not enough to make any diff.
All my tanks run bio-wheels, so I vac the entire bottom (or what I can get to in the planted tank); no worries about ammonia/nitrite spikes.
Btw, were you away for a while Meg? Hadn't seen you in a while.