I dont think you understnading
If you already got your Controller in 6.1.3.4 and thats your default partition, that that means that you are upgrading from 6.1.3.4 to 6.2.x
It has nothing to do with the other partition with is not the defaut one.
When you finish upgrading you will have one partition on 6.1.3.4 and the other on 6.2.x(Which will be the default one)
I dont know if that is what you were asking for?