Intercompany reconciliation checks that what one company says it is owed by another, the other agrees it owes. In Fynease it runs before anything is eliminated, because an elimination on balances that do not agree hides the difference instead of explaining it.
Fynease reads each company's chart of accounts and proposes intercompany pairs between two companies of the same client. You confirm the pairs that are right and dismiss the rest; nothing is reconciled against an unconfirmed pair.
Sales and purchases between sister companies are often recorded to ordinary accounts receivable and payable, with the sister company set up as a customer or supplier. Fynease finds a sister company named as a customer or supplier in the receivables and payables agings and on the ledger lines, and lists each relationship once, one company selling to the other, with the balance on each side. You confirm or dismiss it. From then on the consolidated statements eliminate the balance between them and the month's sales and purchases, and any difference between the two sides is shown as its own line.
This needs the general ledger synced from QuickBooks Online, where each line carries its customer or supplier, or an imported aging. A company brought in by trial balance alone has no such detail.
A correcting entry is booked to the company that is wrong, from the reconciliation itself. It is an ordinary company-level adjusting entry: it is reviewed, and once approved it is written back to that company's QuickBooks Online file. See Write-back to QuickBooks Online.
Charges that repeat, such as a monthly management fee, can be set up once as a template with the lines for both companies, so both sides are booked the same way every month, and sent on to QuickBooks Online like any adjusting entry.
The Cash Balances tab shows every company's cash accounts on any date you choose, from the ledgers: the last month-end trial balance plus that month's entries up to the date. Balances are grouped by company and by currency, with the group total in the group currency at the latest observed closing rate. A company with no exchange rate is left out of the total and named.
It does not eliminate. Elimination happens later, at the group level, when the companies are consolidated. See Elimination entries. For a worked example with a foreign subsidiary and a loan that does not agree, see How to consolidate multiple QuickBooks Online companies.