I'll try to be as helpful and open as possible. Feel free to ask questions.
Yes, you are right that you will have a contract with each brand you bring into the store. You will most likely work with a sales rep from that brand, who will be your contact point for that brand. You will sign an agreement that you will not sell their product for less than what they charge. I guess you could charge more, but that is just dishonest with your customers and will drive people online. You can sell product for less the moment it gets old and the new version comes out. So for example the Ghost 12 is out now. When the Ghost 13 is released you can sell the old inventory for however low you want. A bad thing about this is that manufacturers are in control of this. You can't go lower than them, but they can go lower than the msrp. This is annoying because all the brands now say "we really want to treat our run specialty accounts as our number one" but then the next day that brand is selling their stuff for 30% off because it's labor day weekend. It doesn't happen often but occasionally you'll get customers coming in saying X is selling this shoe for $80 on their website, you look it up and match them, but you as a store lose money on selling it that low.
Someone brought up a good point earlier. Some brands won't work with you unless you've been open a certain amount of years or you have done a certain amount in sales. When you apply to work with a brand they will ask for your financials to see about working with you. So right away I will tell you that Nike and Asics won't be working with you as a new store. Some brands don't care and will open an account with anyone.
Another point that was brought up is that brands might not want to work with you because they already have x amount of accounts in that area and don't want to dilute the brand or take sales away from other stores. Some brands may only have an exclusive dealer in the town you're in.
A big thing to know about working with brands is that each one will have different requirements. X brand may require you to caring 6 models of their shoes. Y brand may require you to order $30K worth of inventory in a year but don't worry about the number of models you carry. Z brand may require you to order $40K in shoes and $15K in soft goods (clothes, etc). Most if not all brands require you to put a certain dollar amount on future orders. Meaning you may have to order $10K in inventory in advance. Which can make inventory management tough. It's a guessing game. You think the Ghost will crush it this year so in June you order a bunch of new colors to be shipped in November. If the new model sucks or customer appeal for that shoe shifts, you may be stuff you a ton of unwanted inventory. Some big stores may not have an issue moving inventory like that, but most stores would. That's why every run specialty store you go into has a ton of shoes on sale. And any shoe sold for more than 40% off, you lose money on. So you don't want to go in over your head with too many models of shoes or even brands of shoes. Each market is different. And each store is different. I've worked with brands where really only one shoe sells like crazy and all the rest on the wall barely sell, so a lot of those go into the sale room. I've also worked with brands that have a ton of brand presence and popularity but none of their product goes out the door because it just doesn't feel good.
I would recommend looking into where you want to open a store. How big is the population? How many of those people are runners? How many stores already sell running shoes? Also consider a large amount of those runners buy online.
Customer service has to be above and beyond what others in your area provide. Most customers could give a crap where they got their shoes. In fact, a lot of people shop based on price. You'll have customers get fitted for shoes and will search online for deals right in front of you.
Also something to know if you were to open a store is who you will be working with. You may be imagining all the Olympic trials hopefuls in your town will be hanging out and shopping at your store all the time. Rarely the case. Those people already get free stuff and never have a reason to shop at your store. Your average customer will be a female from 30-40 years old training going from couch to half marathon. Another large segment will be people who don't run but want a shoe to walk in. And another large segment will be seniors who were told by their pt to get new shoes. Nothing wrong at all with these groups. Just be aware that this is your audience. So you won't be hanging around the store talking about tempo runs and track workouts. You'll be helping people figure out how to keep going after running 4 miles.
A major thing I would honestly ask yourself is does the town I'm in even need a running store? Or it may be, does this town need ANOTHER running store? And also really do the research on what kind of market share you could have. You kind of mentioned profit margins previously, but you need to really want to be working (even weekends and holidays) a lot for a low salary. I've heard this phrased a different way, but would owning a store be worth having a $40K a year headache? And actually you may not even take home any money for a few years before you can start paying yourself.