O.k here's the idea...it's very rough and may need some tweaking.
The 3 most relevant skills for running a business are probably
Contacts; Resources; Scholarship (but maybe there's others that are better....like I said rough draft.
The business is a Character:Let's say the best resources of the party dictates the bars stress track.
The best Contacts is its attack/defense (promotion n' stuff)
Possibly use scholarship as a defense skill as well: accounting and research.
Each "X" time period(month, session, milestone - whatever), play the mini-game. The Bar has to resist an attack of "X". This is just the cost of doing business. The business takes stress and consequences like a regular character but flavour them properly. "leaky roof", broken window, Electrical Fire, Bad Reputation.
If someone has it out for your players(like a godling they may have pissed off), that enemy can add aspects/maneuvers to add to the attack.
Once per time period, the players can, each, do an appropriate maneuver to add to the businesses defense. Contacts to advertise, scholarship to save money with accounting, Deceit to cook the books (if you have forgery or something suitable.); resources to put in that new dance floor etc...
Occasionally, let them "upgrade" the bar by doing an extended tests. Basically, this adds positive aspects to the bar: "security system"; "Hot spot for bands".
These might be extended tests using appropriate skills.
The bar will heal itself of consequences like a normal character, over time provided they do something to "start the healing". A broken window (mild) might need a single craftsmanship or resource roll and it will go away by the next attack.
A moderate of "Seedy Hangout" might require a successful contacts roll and will last multiple "exchanges".
I'm sure someone can throw in some ideas. The thing is this. It gives them the ability to customize their bar, work on it, improve it. It gives them aspects they can invoke over time. It gives enemies a different way of "attacking" them and throwing wrenches at them.
While I was typing:
Money is being tracked for the bar/loan cost purposes, each 'month' they have a quota they have to meet. They can still roll resources to cover the costs if the bar falls short, except the one player who is tapped out for awhile. Works well to set them up to take a job for the paycheck if I am having difficulty getting them hooked otherwise.
Ah, well that'll work since it's a separate "mini-game".