Planting with fish in the tank

Planting with fish in is just fine. For your plants you can use bigger rocks around the base depending on the kind of plant your planting. Do you know what kind of plants your getting?

Andrew

The ones of concern are Eleocharis. I currently do not have forground plants and those are ones that will take some time to plant, and knowing my loaches, the plants will probably be floating by the morning as they have been uprooted. I was thinking about placing some egg crate, or even a plexiglass sheet will some holes drilled in to prevent the fish from swimming near the elecharis until it has taken hold in the substrate. I may also plant some crypts, but those are secondary considerations at this point.

It can be difficult planting a tank with bulldozers like Clowns in it, but once they get established (the plants) the fish usually aren't a problem.

I don't think I would go the egg crate or plexiglass route since you might get anerobic pockets underneath them, and that could disrupt the entire balance of your tank.
I would try the protective rock route instead.

JanS,

When you say anaerobic pockets, would that even occur if a divider was setup to allow waterflow, and CO2 to pass, but keep the fish out? What about if I placed a power head in that area (low enough to not produce surface agitation)? The other thing would be for me to isolate the fish in one area of the tank and wait a few weeks. Any opinions on those ideas?

Yes, that would probably work as long as you don't have it sitting down flat on your substrate and it can get water flow.
If you could get your hands on some Malaysian trumpet snails, they would help keep your substrate worked up a bit too - and then be a tasty meal for your Clown's.