I'm not an expert, but I would say yes, you can do it.
Pairing up batteries is an issue when engine is off with no isolator and no charger, since weaker battery will discharge the other one.
Also, I was advised not to pair up different kinds (ie 6v Vs 12v, AGM vs flooded and so forth...) and this at all times.
I like the relay isolator, it's trouble free. When you turn off the engine, your starting baterry is isolated automatically. No need to access the perko every time to change position.