Yes, having the prefilter is a big improvement since it prevents solid wastes from getting into the gravel bed.
The jury is still out on how any kind of UGF impacts plants. There is some evidence that both can be compromised by the build up of roots in the gravel, impeding water flow through these areas. And, of course, with a UGF, cleaning the substrate is required, and with plants, this can be complicated since you don't want to remove all the nutrients from the plants, nor disturb the root bed with deep cleaning. There is some concern that the constant flow of oxygenated water of the roots may also compromise the plant growth, as well, and there are a some people testing the setups.
You will want to use equivalent setups for bringing the water in. This promotes equal water flow, and discourages 'slow' spots, where the gravel could compact, reducing efficiency. You do not want one side running reverse and the other running 'normal', as this will allow the 'normal' side to build up solid wastes. Running carbon is generally not needed for most setups, so removing it entirely from the system should not have any negative impact on the system. If you are converting from a UGF, you must clean the gravel bed very, very well, or the accumulated debris will be pushed into the water column, creating ideal conditions for a bacterial bloom and cloudy water.