And another thread is raised from the dead!
I think I would be tempted to first look at your set up and draw a wee diagram showing what is connected to what, since there are a number of ways it can be done. (My post of a couple of years ago mentions some of the variations.)
I have distinct reservations about the "switch to both before starting" advice. As you have already identified, the first thing that will happen is that current will flow from the (hopefully) fully charged cranking battery to the partially discharged domestic battery. It also rather defeats the point of having specialised batteries for each job. Assuming you have the simplest wiring arrangement, i.e. alternator, starter and loads all connected to the common terminal, cranking battery connected to "1", domestic battery connected to "2" then I would recommend the following starting procedure:
1. Switch to "1"
2. Start the engine
3. After a few minutes of running at sufficient revs to charge batteries, switch to "both", then to "2": delay doing this if the engine was difficult to start or it has been some days since batteries were charged, since the idea is to first replace the cranking energy used plus the starting battery's self-discharge.
When you shut down the engine leave on "2". This should ensure you keep your cranking battery fully charged while discharging the domestic.
The key point is remembering to make the switch at the right time: some of us are better at this than others. A properly installed VSR makes the process automatic and saves having to remember. A smart controller can significantly reduce the time taken to charge. A battery monitor can give a very good indication of what's going on, but a simple DVM will be much better than nothing.
I assume, in the above, that your 1-both-2 switch is make before break. It should be, but check with a meter to confirm. If it is in fact break before make then you risk blowing your alternator diodes if you switch with the engine running. In that case I would recommend replacing the switch, or taking the opportunity to overhaul and improve the whole set up. Alternatively, you would have to switch to "both" before starting, then not touch it until the engine is stopped. Which, given the manufacturer's advice, does rather make me wonder...