I took Cruz Del Sur on the exact route you are seeking and booked my tickets online. I agree it is a little confusing but I eventually figured it out by emailing them - they responded right away and told me which bus to book. If you don't speak Spanish (I don't) here's a tip - write your question out and put it into Google translate, then send that. You can then use it to translate their response. Worked pretty well for me.
Cruz Del Sur's buses were well maintained and comfortable - I highly recommend booking a first class ticket. Doesn't cost too much more and is well worth it for the larger seats, leg rests, and extra space. Also, a first class ticket will get you access to a waiting lounge at their Lima terminal. The lounge is nothing special, but was a nice quiet place to retreat from the chaos of the terminal while waiting for our bus. Food is available inside the terminal.