don't listen to 69 love songs like you would do with canon rock stuff. it's massive. listen to it a CD at a time, or even some songs sporadically here and there. it'll grow on you.
or as avery says, i could just recommend 'The wayward bus/distance plastic trees' for a double dose of stephen merritt's brilliance
Personally, I think the best way to listen to it is just have a playlist of all 69 songs and put it on shuffle.
I agree it's not an album that's designed to be listened to from start to finish though, but neither is it an album that's designed to be listened to from start to finish particularly (in the CD booklet, the tracks are listed in alphabetical order, not track order).
I think one of the main points about it was that it was supposed to be an antidote to the rock canon opinion that you have to listen to albums in order and can't take from it what you want. Instead, it's more a case of being a collection of a LOT of really great individual songs, rather than really being an actual album. You're supposed to play them as you wish. I mean it has more great songs on it than in some legendary artists' (Joy Division, Nick Drake, The Stone Roses etc.) entire discography.
Like dreamcoil says though, it's an album that has that grows on you, of course, if you don't want a "grower" then that's not for everyone which is perfectly fine, but it's one that is well worth it when it does. I've been listening to it for 4 or 5 years and there are still new songs which jump out at me, I've only just realised just how stunning "Abigail, Belle of Kilronin" actually is.