Whoa, another can of worms
With bookshelf speakers (or surrounds, or 99% of centers) you want to set them to "small" because they can't handle the bass. It's the M60s where you have options, because they can go quite deep on the bass. There are three options, each with pros and cons, each with its own fan club :
1. Set the mains to small as well, typically crossing over at 60-100 Hz. The argument for this is that the sub will still handle bass better than even the M60s and the system can play both more loudly and more cleanly this way. The arguments AGAINST are (a) picky music listeners sometimes find the crossover region between sub and mains doesn't sound right (you don't notice with HT) and (b) you can argue that by having bass split between M60s and sub you get more even bass distribution than you would with a single speaker (sub) carrying all the basee.
2. Set the mains to "large", set the crossover for mains to 40 or 60 Hz so the sub comes in where the mains start to roll off naturally, but keep a higher crossover for center and surrounds because they can't go as low. The advantage of this is that the mains carry pretty much all the bass for music applications but the sub is there for HT. Cons are that more tricky setup is required, it's hard to match the sub xover with mains rolloff, and not all receivers will do this.
3. Set mains to large, feed all the bass to the sub as well, resulting in arguably too much bass in the crossover region. Arguments for this are a bit more tenuous, including "hey, I paid for bass and I want as much as possible"
On the serious side, if your room acoustics are bad one could argue that this arrangement will put a serious dent in bad frequency response dips -- the problem is that it doesn't do anything for the peaks.
The holy grail IMO is to have a receiver which can switch setups depending on your source and decoding modes. My HK is set up to use option 1 when playing DVDs and option 2 when playing music (CDs, FM etc...).
I imagine some people switch back and forth between options 1 and 2 their whole life, occasionally using option 3 when they screw up the settings