How to parse two seperate hash files in the same attack?
Is it possible to make Hashcat run through two separate hash files and output to two separate files in the same attack? Or would I have to compile them as one and sort it after?
Pretty sure you have to run seperately or parse after since only one output file is supported, sorry....
Yes, best way is probably to merge hashes, do all the cracking that you want and then re-crack each list separately using only the passwords that you have found. Oclhashcat has no way to keep track of what hash goes in what list and can't load two hash lists anyway.
You don't necessarily have to re-crack each list.

Merge each hash file, but retain the original copies. Crack the merged list. Then use --show against the original lists.