Account for 1120S balance sheet discrepancies by adjusting additional pos in capital or retained earnings?

You likely put something to the wrong place and/or didn't enter something at all. That's about the only way you can be "out of balance."

Can you give us your data, as examples? For instance, this: "this taxpayer bought and wrote off a 6000 vehicle"

Is often entered incorrectly as the purchase going directly to Expense. Then, the depreciation is also going to expense. Or, the Loan payments were posted to Asset value, and there never was the debt entered. These are common mistakes.

You show the loan because it still is owed, no matter the situation for the asset. Example:

Asset basis $100,000

Depreciation -$100,000 <== this is offset to Expense, so it affects the P&L, as Net Income which is part of Equity

Debt balance $85,000 <== pretending there was $15,000 downpayment

Equity $15,000 (from the downpayment) + $85,000 (the loan balance) + negative net income $100,000 (the Expense entry)

Assets = Liab + Equity

$100,000 - $100,000 = $0 asset

And Equity (which also is called Net Assets) = $0

That's in balance.

"Is there a better option?"

Yes, you need to have an in-balance working trial balance before you even start the return.

It should show:

Asset $ 100,000

Accum. Deprec ($ 100,000)

Truck Loan Payable 

IF down payment made

Cash ($ xx)

Truck Loan Payable $ xx

*************

Deprec Exp on P&L $ 100,000

ignoring ALL other income/expenses...the P&L will show a ($ 100,000)  which reduces the Retained Earnings on the Balance Sheet.