| You don't have to remove the fish if you do this slowly.
The majority of the good bacteria in the substrate is on top.
Taking out small sections over a period of time shouldn't do any damage to the good bio.
I would sypon out no more than 1/4 of the sand out at a time and less would be even better.
The longer time you take to do the switch will work in your favor.
Remove and replace it by section. For example start in the back corner, sypon out sand and replace that area with gravel.
To put the gravel in the removed sand's place, be sure and rinse it first. Slowly, lower the gravel by the cup full to the empty area.
When your cup of gravel is on bottom of the tank, slowly pour out the gravel on the tank bottom.
If there is some sand left around the gravel, it's no big deal unless it's a totally different color.
The sand will work it's way to the bottom, under the gravel and disappear.
You may get some clouding during the switch,
but the filters should be able to clear that in a few hours, since you are doing a little at a time.
When you replace your substrate, remember, you don't need 3" of gravel.
The lesser amount you actually have, the less is there to catch and hold debris.
I only have about 1-1.5" of substrate in my tanks. It makes maintenance easier.
If you are worried about holding down fake plants, or having thick enough substrate to plant in, use small rocks at the base of the plants to weight them down.
hth,
alicem | 
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