First of all I'm a firm believer that everybody should use the setup that is fitting their individual situation. As an "outsider" I find that many people here have a "standard" situation due to the fact that they operate their real estate business in a "normal" way simply because they are resident in the US and might actually do things on their own simply because they can. This results in a "standard" approach. Don't get me wrong: nothing wrong with that! And good for them as it's fairly simple. Then there are people like me where many of these aspect do not work as I'm not physically in the US.
I therefore thought I'd chime in @Brandon Turner, even though I feel a bit "puny" when reading the numbers that are thrown around (56+ units, etc). Then again, I do have some 9 doors in 6 buildings now, and ultimately the principle is the same. Also, I have a mix of what's been described here, I think:
@Curtis Bidwell and @Simon W.: this is what I do too. However, since my operating LLCs only own 1 property each in praxi I therefore do have 1 account per property (for those owned by an LLC). The LLC owning a multi-family consequently also (only) has 1 account. Having one bank account is really required for the LLC to have any effect with respect to it offering liability protection.
Now, since these LLCs are all owned by 1 parent LLC (Holding, or whatever you want to call it) and this parent LLC being a single member LLC, the accounting ultimately is, in relation to tax matters at least, for me as a private person filing 1 tax return. So one should consider the individual situation with respect to that. If the LLCs were partnerships or S-type then this would be very relevant and somewhat different.
From a practical point of view: Since the parent LLC has a bank account as well, I can simply open the accounts of the underlying individual "children" LLCs as sub accounts of that parent's LLC bank account. Makes it very simple to open (or close) an account, I only have one login (yes, still different checkbooks which I never use anyway as I do everything online or my PM takes care of it) and still everything is separated legally with respect to each LLC having its own bank account. No co-mingling funds there, especially not with my private ones.
In addition, my LLC units are all managed by a property manager. Yes, that poor chap has to account for everything individually: Rent for property A goes into checking account of property A LLC. Bills are accounted to the individual property, i.e. LLC, and so on. Just as he would have to if these units were owned by nine different people.
And my properties are financed (= property and insurance taken care of by bank). So for me there are basically none of the practical issues described by @Justin R., who does, however, have a very valid point when looking at his individual situation.
Now when it comes to units held in my own name: I see no real reason to keep separate bank accounts as I'm on the hook personally anyway. That does not mean that I don't keep separate accounts in relation to the operating aspects. I need to know what the figures are for each individual unit. And the latter has nothing to do with a bank account. For this situation I can really see the practical issues pointed out by some here. However, maybe 1 LLC with a master bank account could make sense then, simply to facilitate your account, ehm, accounting. :-)
How do I keep track of all this? I love Excel. It's my work horse when it comes to numbers. As I'm a cheapskate ;-) I didn't want to buy no fancy (= expensive) software. Since I started with 1 Condo a couple years ago, I simply created an xls file with appropriate sheets to e.g. calculate cash flow while factoring in the individual monthly expenses of the property (really: the unit) and whatever else is necessary. This is all automated thanks to references within the xls file. Heck, I can even consolidate these individual xls files in another overarching file to see the overall figures of my "enterprise" (just make sure you got your folder setup figured out before doing this, otherwise references turn into a mess...don't ask me how I know). With this I was simply able to scale for each new unit: copy xls file, name it after the new property and set up sheets depending on the amount of units in the property. Yes, the details will change depending on the type of transaction and the amount of units and so on but changes are minimal, especially once you have run into that situation once (like going from 1 unit to a multi-unit: a bit of work, but from there on you can simply copy that particular multi-unit excel and use it for another, new property). Very simple. And cheap.
Now, would this excel thing work if I were to do several deals a month and/or hundreds of units? Probably not! I would have to find something that takes away the need for adjustments in that regard. But this is currently not my situation and I cannot envision it to ever come to that. And if so, I would also have a lot more time to deal with this as I would then not have a job anymore as an employee but would do this full time.
I found what (currently) fits me. Maybe some of the aspects are of use to others reading this.
And now I shall apologize for this loooong post...