(On the side) If I'm right about the specific comic book store you're talking about, it's not a good place to hold a tourney. I'm not exactly sure, but ever since I've heard of Albany and that comic book store (which was back in 04) I've heard NOTHING but bad things about it, and I still hear about it to that day. I AM HOWEVER TALKING ABOUT A CARD SHOP, so if you literally mean a comic book store (which would be a different place), then ... well you just got some forewarning about this card shop. (Ask Matt about it (Radioshack, as I call him). I know a bunch of the TCG players would frequently come up to warner robins for the tourneys up here)
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ANYWAY, beside all of the instate talk.
You really just have to sit down, talk to the owners of the store, let them know what's up and ask if they're willing to help out.
Some places love to do stuff like this because it will drum up some business for them. A comic book store, although sometimes very cluttered, is a pretty good place to have a tourney (for them) because most of the players are intereested in their product.
First and foremost; you need to know wtf you're doing. Even if it's your first time, you're nervous, or you don't have a real clue wtf is going to happen, you need to act like it when you talk about it. If you come up to a business owner with something like this, they expect you to know EVERYTHING you're going to be doing, so you have to be ready.
-Explain to them how they're going to get their cut of the money (be it venue or pot cut (FOR THE LOVE OF GOD PUT IN THE POST IF YOU'RE DOING TO DO A POT CUT OR I WILL KILL YOU)
-Take time to go to the store, check out the place, and walk through a layout with them. Ask them what spaces you can move, talk about equipment (whether you're using theirs or bringing setups), etc etc. You obviously want a no traffic (or low traffic) area. Explain to them what you need to make it run and how you're going to do it. If they've never ran a game tourney in their store, they have no clue wtf needs to be done.
-Explain to them HOW you're going to run the tournament. First off, let them know that you're ACTUALLY going to do it and you're not asking them to do anything outside of their normal business. I've seen too many times where somebody goes into a place and basically throws it onto the owner (or random clueless female employee, lol) to run a tourney and they have NO clue wtf is going on. Give them a quick run through of the format you'll be using (or potential formats, if you need to bump down to doing Round Robin), show them TIO if you have it, etc etc. Again, this leads into showing you know what you're doing and gives the owner more confidence in allowing you to use their space without causing a hassle.
Beyond that, you really just need to be clear about store policies. If the owner has a rule about outside food or drink, cursing, etc etc, you need to go over some things with him. If there's a small occupancy rate (whatever that's called), you might have to ask for some wiggle room or find another place.
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All in all, you're really going in there making a business proposal to them, so you have to act like it. You can't go in there giving the impression that you're some punk kid looking for a place to hang out and trash. You need to sound like you're a businessman who's done this before, regardless of what follows afterwards.
And I promise you, unless you wind up with a REAL small tourney the first time (i'm talkin like, 4 man tourney), you'll have some rough spots first time through. It's ok, you live and learn. You just want to avoid major screw ups.
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Confidence, firm handshake, all that nonsense they tell you, yada yada. XD
Edit
*looks up at NSM's post*
.... **** I type too f***ing much. :/