I'm going through this now. I'm trying to figure out the best overall business structure. I currently have 2 LLC companies. I set up one for management and marketing. I have another that is currently holding 3 duplexes in the same state. I've ended up doing wholesaling from both of them, and a flip from each of them. I keep separate books for the 2 LLCs, and my CPA enters the complicated and the year end entries, and prepares and files the tax returns. So this makes 3 annual tax returns (2 LLC; 1 personal). I'm now buying a larger business in my area, which will be a 3rd LLC (and 4 annual tax returns). I have credit cards and lines of credit in the name of each of the businesses. I plan on buying a lot more cash flow property.
The problem with having a lot of LLCs is the management and maintenance of them. A separate LLC for each house or property isn't practical. You need to do a separate tax return for each one. You need to make sure you are doing the proper formalities for each LLC for the asset protection. If you are sued and have not followed all the formalities, then the court can pierce the corporate veil and there goes your asset protection. So you need to file the Articles of Organization forms with your state's Secretary of State. Answer the questions properly to have good asset protection. Make sure you have a separate Operating Agreement for each LLC, and follow it. If you don't know how to do the A of O and OA, then hire an attorney. This costs some extra bucks. Set up a separate checking account for each LLC. Make sure you hold title to each property in the name of the LLC that owns it (or leases it, in the case of Lease with Option to Buy).
As I'm sure you know - you need to make sure not to co-mingle money. So keep your income and expenses associated with each property in the LLC it is owned by. DO NOT pay personal bills from your LLCs. If you are low on capital, take a distribution from 1 company, and make a contribution to the other 1. Or have Company 1 loan Company 2 money, and document it properly with a promissory note with market rate interest. You have to treat each company as a separate entity, which it is.
The more LLCs you have, the more complexity you have. This creates more opportunity for errors on your part. The paperwork can get away from you. I've been using LegaLees (www.LegaLees.com) for a few years, and it's really been helpful. Lee Phillips gives practical advice. He advises breaking up your businesses into a few chunks that make sense, and managing them well. If you have properties in separate states, have an LLC in each state you own property in. If you buy a big business, or have another business function or set of activities, create a separate LLC. For example, rentals in one LLC (passive income), and a contractor business in another LLC (active income). Perhaps limit the value of assets in each LLC to about $500k, except if you have a bigger biz (like storage units), then it may be valued at more than $500k, and that's ok. His advice is that it's better to have 1 or a few well-managed LLCs that follow all the proper formalities, then a whole bunch of them that might not be well-managed.
Increased insurance coverage is not that much more (I'm looking into that, also), and is much more simple than a lot of LLCs. I'm also looking into an umbrella policy. Insurance will protect you from a lot of things that can happen.
Besides the cost of the annual LLC fees, you have to take into account your time managing all the paperwork and keeping things separated, AND the cost of legal fees setting this stuff up, AND the annual filing fees, AND the cost of help from a good CPA, AND filing the separate tax returns.
Check out the website www.LegaLees.com. Buy the book Protecting Your Financial Future for about $20 to learn more about this topic. It teaches with stories rather than boring, technical, legal speak (although it's still a lot to digest). It will also teach you how to work with attorneys and speak their language. Watch the LegaLees YouTube videos on LLC topics - they have a bunch of them - and this is free, general, practical advice from an attorney. As I said, this was very helpful to me.
Hope this helps. Good luck!