I have an MP-1 which does not use the 12AU7 so I cannot compare the relative influence of those tubes with the 6SN7.
In the MP-3 I believe the two sections of each channel's 6SN7 are part of its circlotron output with each cathode in a tube handling one-half of the wave form. (Hopefully Ralph will correct if thats wrong. :-) Thus, it is v. important there be a decent match between the sections within that tube, and that the tube be quiet. As Tvad notes, 'quiet' is a critical attribute - moreso for the preamp than for the amps - so a dealer (such as AndyB at VTS and others) who will screen for noise may save you some money in the long run even if he charges a bit more for the tubes.
The brand/vintage of each channel's 6SN7 will have a real impact on the preamp's sonic character. Some contemporary tubes are 'not bad' - eg., I and others who've tried the Electro-Harmonix 6SN7 find it tends toward a timbre not far from a Sylvania GTB. However, quiet NOS versus a Chinese or Russian 6SN7 in that position, is, imo, not much of a contest and for me NOS are worth the extra rubles. While you can spend a lot of money on the more exotic 6SN7 varietals (bad boy chrome domes, round plate tung-sols,'W's, etc.) a couple nice Ken-Rad, Sylvania, Raytheon, or RCA GTs/VT-231s shouldn't break the bank - especially if you start with used tubes to learn your own sonic preferences. If you haven't seen the head-fi 6SN7 thread, you can read it
here.
Fwiw, I've found Herbies tube dampers do their thing nicely on the line stage tubes as well as in the phono section. I use them on 6 out of the 10 6SN7s in the MP-1's line stage, and on 6 of the 8 12AT7s in the phono section. Best of luck tube rolling your new MP-3!
Tim