Yes you can just put the charger onto the leisure battery terminals without disconnecting anything - you don't have take the terminals off, just make sure you connect the charger cables the correct way round.
I disagree with Tosh, but then he has had a lot of grief from flow controllers, so I don't blame him advising you the way he has. However, this time removing the flow controller won't get down to the basis of the problem. Infact, removing the flow controller will aggrivate the problem further, because your battery isn't being charged up enough.
So the first step is to charge your battery up and that will get you going fine tomorrow.
The second thing you need to do is order or buy a 10 amp on/off switch from an electrical sales outlet. This will be fine.
http://www.screwfix.com/p/lap-1-gang-10a-switch-ip55-240v/47152Now you want to put this next to your controller so you can switch off the current from your leisure battery to your Varistream. So this will be an isolator switch. The problem with the latest Varistream is that they use current even when they are switched off.
We found that a new fully charged 85 amp Numax leisure battery was being drained to a 75% charge just lying idle for a week. At the end of the day just switch the switch off - end of story.
The very reason you are able to let the van engine run and charge the leisure battery a bit shows that the split charge relay system is working correctly.
I have fitted a volt and amp meter to my system to see what actually happens during a normal working day.
With our Varistreams the higher the pump flow rate the more current (amps) the motor draws. So I would guess that with Tosh's pump running flat out, his pump would be drawing about 8 amps, whereas ours will be drawing around half that, depending on our flow rate setting.
If we assume that your pump is drawing 4 amps per hour and your pump actually pumps water for 4 hours through the day, then the pump will have drawn 16 amps of current from the battery. In theory this means that if you have an 85 amp battery you will only have 69 amps left.
Even when my battery is half charged my alternator settles down to a charge rate of 8 amps when recharging the leisure battery. In theory this means that your van needs to be charging your battery for 2 hours to replenish what you took out. (Unfortunately it isn't as simple as that as the battery will only accept a smaller and smaller charge as it gets fuller. I once read in an Australian camper van article that someone estimated it would take a road journey of 750 kms to recharge an 85amp leisure battery via the vans alternator.)
Now it usually takes me 10 minutes to drive to my first house maybe another 10 minutes moving the van etc and 10 minutes driving home. So using the above example, I am taking 16 amps put of the battery and only putting 4 amps back in the day (30 minutes driving at a recharge of 8 amps). So you can see that within a short period of time my battery would be flat if I didn't supplement it's charge with my battery charger.
If I get stuck in traffic, thats good for my leisure battery as the van still charges my battery at the same rate idling as it does at 3000 rpm on the motorway. So the longer it takes you to get home, ie the slower your drive, the more charge you are putting into your leisure battery and also saving fuel.
If you do a search, I have commented on leisure battery charging on numerous occassions, some of which are relevant to you.
Hope that helps.