Yes, you could certainly "clear out" your books at the year end. On January 1, your net income is automatically transferred to Retained Earnings. You may also have a balance in Opening Balance Equity and presumably your checking account. Assuming you have no debts or other assets, these should be equal. You could simply just do a reverse entry in QuickBooks -- zeroing out those books. And put the opposite entry into this other accounting software so your balances are all the same. So your cash will be (for example) $1,000 -- and Owner's Equity will be $1,000. Don't bother with Opening Balance Equity, that's merely a QuickBooks account and really shouldn't exist.
And if your accounting software is good, as QuickBooks (believe it or not) is, it'll warn you when creating a transaction against Owner's Equity. This is because it's unusal to post anything to it except by those who know what they're doing.
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Evan L.
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