Well sorry I can't help you much. I have all girls...for that very reason...
but I have babysat males before & understand what you're going through. Clearly, he marked because of all my girls in the house but after the 1st day, believe it or not, he didn't mark any more. I just made sure I took him out a couple more times than I did my girls. He marked my shoe rack at the door, a column in the living room, and a case of deer park water near the kitchen
weird choices I know...LOL
Anyway, the only thing I was going to mention is that even though you got the couch cleaned, you may want to make sure you also scrub/clean around the floor/carpet area where he marked on the kitchen..drops also hit the ground even though he marked the couch so maybe that's why you're still smelling it a little.
Other than that, baby gating him while you're away(hopefully it's not too long) & only letting him out and about when you're there to keep an eye on him is a good idea.
Best of luck!