Planted Tank Obsessed
Join Date: Jan 2012
Location: Inland Empire, CA
Yes, you should cap it. All the tank I've seen (and mine as well) have a cap. I add it before filling the tank and haven't gotten any dirt particles in the water as of yet. I used 1" cap on my tanks.
I would get a bit of small airline tubing and try to suck it out with that. That shouldn't disturb the water, as long as it's long enough you don't need to put your hands in, and it should be gentle enough for plants controlled. If the leaves are near the substrate it might suck up a little from there but it shouldn't kick it up everywhere.