Mercury vs Relay: Choosing Banking for a CPA or Bookkeeping Firm

Most accounting and bookkeeping practices run a single legal entity with a predictable, recurring revenue pattern: retainers or monthly bookkeeping fees land on a schedule, and the swings are smaller than at a typical services business. That predictability is exactly the environment where Relay's envelope structure earns its keep. Route a fixed share of every incoming retainer straight into a payroll sub-account and another into a tax reserve sub-account, and your partners never have to wonder whether this month's distribution is really available or already spoken for.

A firm with more structure, a holding company plus an operating subsidiary, or separate entities for a staffing arm and a consulting arm, gets more value out of Mercury's entity-level account architecture and its API, which a technically inclined ops lead can use to pull balances into an internal dashboard rather than logging into multiple portals every morning.

Match your firm's own account to its structure:

• A single entity with predictable retainers suits Relay: route a fixed share of each retainer into payroll and tax reserve sub-accounts.
• A holding company plus an operating subsidiary, or separate staffing and consulting entities, gets more from Mercury's entity-level account architecture.
• A technically inclined ops lead who wants balances in an internal dashboard instead of several portals is a reason to choose Mercury and its API.
• Partners who want certainty that a distribution is really available benefit from dedicated sub-accounts, whichever platform you pick.

Before you decide how much banking automation is worth paying for, it helps to know what your staff time actually costs. The median annual salary for accountants and auditors nationally is $83,680¹, with the middle half of the market falling well above and below that figure depending on experience and region. Every hour a senior bookkeeper spends manually reconciling a client's sub-accounts or chasing a missing 1099 is an hour priced against that number, which is the real argument for automating reconciliation and filing wherever a tool can do it instead.

If your firm handles accounts receivable or advisory work for clients, collections speed is a live issue across almost every client industry you touch. The average small business now waits 28.8 days to get paid² from the moment an invoice goes out, and that average hides wide swings by sector. Clients in business and consumer services tend to run notably slower, carrying receivables around 67.3 days³, while a retail client collects in under two weeks. When you're advising a client on cash flow or setting up their own multi-account structure, benchmark their receivables against their specific industry rather than a single blended average, since the gap between a services client and a retail client can be a full month of working capital.

Two categories of tooling save the most staff hours across a typical bookkeeping caseload. The first is 1099 and W-9 compliance: collecting W-9s from every vendor a client pays, tracking which vendors crossed the reporting threshold over the year, and filing electronically instead of by hand. Tax1099 automates that workflow directly off client bank transactions, which removes the January scramble of reconstructing a year of contractor payments from memory and spreadsheets.

The second is accounts payable itself. BILL automates approval routing, multi-entity payment scheduling and vendor disbursement in a way that keeps a partner's eyes on every payment above a threshold without that partner manually approving every routine bill. For a firm managing AP on behalf of several clients at once, standardizing on one AP tool across the caseload, rather than learning each client's own patchwork, is usually worth more than any single feature either tool offers.

It's worth keeping the shape of the small business population in mind when you're advising clients on banking structure. Nonemployer firms, businesses with no staff beyond the owner, now make up the large majority of US small businesses, numbering nearly 29.8 million against roughly 6.4 million firms that carry employees⁴. A solo client with no payroll has genuinely different banking needs than an employer client managing a biweekly payroll run, and a one-size answer for "which bank" undersells clients on either end of that split. The nonemployer client usually just needs simple envelope budgeting for taxes and estimated payments; the employer client needs payroll timing, benefits deductions and a bank that plays well with a payroll platform.

This split also shows up in how much onboarding effort a new client is worth. A solo nonemployer client rarely needs more than a single checking account and a tax sub-account set up in an afternoon, so standardizing that setup across every solo client saves your team from reinventing it each time. An employer client is worth the extra hour of setup work: mapping payroll cadence, benefits deductions and any owner distributions into separate sub-accounts up front avoids a scramble at the first payroll run, and it gives you a cleaner starting point when that client eventually asks you to reconcile the books.