Not that I'm an expert, fairly new to this particular bot (slippery little critter he is)...
But I run multiple folders, one for currency pair AND also separate strategy, so...
example folders: pay-btc-bb, pay-btc-bbgain ... etc
I do this because, for example a bb strategy for one pair may well be different to another pair, so easy to tune on the fly and only affect that one pair.
I just create shortcuts of each .exe pointing to it's relevant folders, shortcut named same as the folder, so easy to start any instance of any pair / strategy, all from one place.