Roth Conversion - how to handle loss of princilpal

I have 2 IRA's. one has 100k but the cost basis is 200k (so 100k loss). the other is well in the black. If I convert the 1st one entirely into my Roth account, and say 500k of the 2nd one do I need to pay tax on the entire 600k or just 500k due to the loss?