Shouldn't be any probs using a trickle charger while the battery is still connected however if the battery is very low then it may not charge up enough. These chargers are only really designed for small capacity batteries or keeping one topped up through the winter as you would with a bike. Better to take the battery off and give it a test and a charge using a bigger charger. A normal full size battery charger, even when set at 12Volts, can often put out up to 16Volts which is too much for the delicate electronics so best not do it on the car.
Only take the battery off a P38 if you have the EKA reset code or access to a diagnostic unless you use a memory saver. You could of course connect e.g. a bike battery to the connectors using small jump leads while the main battery is off. This will keep power in the system and keep you from having to reset every window, sunroof, radio etc etc. Some P38s have a back up alarm which will go off if you disconnect the battery but as long as you keep power in then that should be ok.
Removing relays is ok while the battery is on generally but maybe not while the engine is running however be careful what the relay is for, e.g. you wouldn't want to leave the keys in the car when you disconnect or re-attach the central locking relay just in case it goes, "thunk - ha ha, I've got your keys!!!" (In fact never leave keys in these cars even when everything is working for the same reason.)