More detail
The problem is visibility. If both shops collect into the same number, your daily totals tell you nothing about which branch is performing or where money is leaking.
Software that tags every payment to a branch, cashier and shift gives you per-shop numbers regardless of how many M-Pesa numbers you hold, so you run each shop on real figures.
Free tools for this
Related questions
How do I track sales per branch?
Use a POS that records each sale against a branch and cashier. Then your reports show takings per shop even if the M-Pesa number is shared.
Veira gives Kenyan shops one calm app for selling, M-Pesa, KRA eTIMS and stock, with a free terminal. Book a demo and see it set up for your trade.