The central issue you’re trying to solve for when you operate in more than one state is making sure that your books accurately account for the state in which revenue is earned. This is the starting point to make sure that you allocate the correct income figures in each state that you operate in, and thus file a tax return in.
Additionally, there are a number of factors that can create nexus in a given state. If you have nexus in a given state, you likely have a requirement to file a tax return in that state. The factors are not always straight forward, they vary by state, and you can actually have a requirement to file in a state that you do not even have a physical presence in. Some of the factors that can determine if you have nexus include where your employees and certain independent contractors are located, where your offices are, where you store products/merchandise and a host of other nuanced situations. For those in the trucking industry, there are a host of considerations that must be evaluated to determine which states you need to file tax returns in and how you must allocate income to those states. Any income or deductions not allocated to those states that are outside of your home state (where you are incorporated and likely have your headquarters) typically default to said home state.
From a bookkeeping standpoint, it is often valuable to have the same firm that does your taxes (and hopefully tax planning) also do your bookkeeping so that they can create your books in such a way that makes tax filing easier and more accurate, along with helping you prepare for any tax obligations in the various states you operate in.
Ultimately, you should be looking for a CPA firm that has experience in dealing with clients nationwide as they will inherently understand the various state-by-state issues that will need to be considered and addressed by your company. And it should be a CPA firm versus an EA (Enrolled Agent) or an unlicensed individual/firm. Those who don’t carry the CPA credential often (but not always) don’t possess the needed skill and experience to handle these issues correctly.