I was wondering about the pickups i am wanting on my new guitar. I haven't bought it yet, and have not even started looking at guitars themselves. Right now I'm just coming up with what I want the guitar to have. I have a pickups question.

What is the tonal difference between a HSH pickup setup and a HSS? I can't decide which would suit me better, but will play both (hopefully) if I can find a guitar set up that way at my local store.
24 people looking at your post, no one responding. It is a bit of an impossible question, or should I say, a good question for which it is not possible to write down a proper answer. Language is ill equiped to describe tonal properties. Someone could give it a try and tell you about the 'beefy' versus 'thin' here and 'woolly' versus 'sharp edged' there, but how would that help you? All the words one could use are ment to describe sensations of touch and vision. Read a musicians magazine and you know what I'm talking about. On top of that, there are a lot of other factors involved.
I'm afraid there is only one thing you can do. Go to the shop and test as many guitars as they would allow you and then go to the next shop and start all over again. It's the path we all have to walk.
what i would say is this:
if you have a humbucker in the neck, it will sound clear and smooth, with a (perhaps) distinctive glassy sound to it, less suited for classic bluesy stuff / strat-ish sounds, whereas a single will give a dirtier but perhaps equally as glassy just not so smooth sound, for stuff like hendrix etc.

i think (personally) that HSS is the most verstaile, but thats opinion

hope that helps

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