Im quite confused, so lets go slow..
-set you amp up for you clean sound; if its 40w then it should be penty loud to make your ears bleed, but the volume on your amp doesn't determine the gain produced (unless you're using a valve amp, which Im guessing you're not), just the overall volume. the gain control will take you from clean to distorted as you go from left to right. set it at bout 11 o'clock for cobain clean
-with a boss distortion, there is not much extra volume on tap so there won't be much of a volume 'jump' as maybe you'd like; the cleaner you set your clean the bigger the volume jump when you kick in the distortion pedal (with my bro's DS-2 'unity gain' is at about 3 o'clock, so set it anywhere after that for a boost)
-serisouly consider other pedals; the ds-2 is more versitile than the DS-1 (although i dislike the turbo setting a lot) but still very limited if you want to play anything other than grunge. My boss BD-2 blues driver has loads of gain, especially with humbuckers, and achieves 'unity gain' at about 11 o'clock, so you can have a HUGE volume jump if you wish. Also proco RATs and especially TURBO RATs have loads of volume on tap and will be much much more versatile than the ds-1 or 2 (to listen to it on record, try Sonic youth-Dirty, yeah yeah yeahs-fever to tell and foo fighters' self-titled debut: grohl loved them before mesa came knocking)
