In my experience, both tubes affect sound quality, but the driver tube (i.e., 12AU7) is about 75% of the equation. In my "speedballed" Crack, I've switched between a 5998, 6080, and 6N13S (Russian 6AS7 substitute) and there is most certainly a difference in coloration and bass damping over my HD650's. The lower Rp of the 5988 and higher gain seems to yield much less "tube" sound or distortion vs. the 6080, and especially the 6N13S, which appears to be a rather un-linear copy of the 6AS7. It sounds warmer, with a smaller soundstage and flabbier bass, when compared to the 5998. How much of this is due to the Z-out going from 120 ohms to 70 ohms with the 5998 is unknown, however.....
I've also played with driver tubes. I'm now using a clear-top 12AU7 in the driver socket, which is very detailed and smooth. 12BH7's tend to sound much "bolder" and have a bigger soundstage. Other 12AU7's seemed kind of "blah" or boring to me. What's really interesting is how you can team the output and driver tubes for a certain sound - i.e., use a warmer, higher distortion 12AU7 when using a 5998, and a sharper-sounding, less warm tube (such as a 12BH7, E80CC, etc) when using a warm-ish 6AS7 or equivalent.
For what it's worth, I've found various changes to not make a huge difference in sound with the Crack - everything sounds good! I'm not sure if that's due to the inherently low distortion of the cathode-follower, OTL design, the gargantuan film capacitors I shoved under the hood in place of the stock electrolytics, or the Speedball plate loads. Regardless, the Crack makes for an exciting listen, and the fact that almost any tube (or combination thereof) sounds good on this thing is definitely a plus in my book.