Regardless of whether you have a reasonably big lift out battery cover in the floor, the carpet has to be removed out of the way, and in some cases the alligator clamps can be very close to the chassis.
A few years back this annoyed me to the point where I decided to make the process simpler, safer and quicker.
I flush mounted a plug in the top of the floor, and fitted the same plug on my battery charger. The floor plug is permanently wired to the battery, and the connection process just requires lifting up the edge of the carpet and "plugging" it in.
Pictures of the parts are below:
The charger plugged into the flush mounted floor plug
The flush mounted in floor plug
The wiring set up for the in floor plug