Keeping track of expenses and payments to a company credit card

I am running QB 2012 - when I reconcile and click OK it does not ask me that question, it asks if I want to make a reconcile adjustment, which I do not. And when I go to just Write Checks, I can't seem to match up the credit card with the expenses. Any help would be greatly appreciated.

Your beginning and ending balances in QBO should match with the Credit Card statement for the month you are reconciling. When it doesn't match, it asks to make a reconciliation adjustment

The Beginning Balance doesn't have to Match; if you recreated any transactions, and you affect their Reconciled status, it won't match and that doesn't mean something is wrong. It means something got Changed. Example: One entry should have been two, or two should have been one. As long as you put in the right info, it will Re-reconcile just fine without any Adjustment.

If you recreate any transactions or if you affect their reconciled status, the ending balance doesn't match, then we have to undo reconciliation and then redo it which means something is wrong.
Please correct me if I am wrong.

If you recreate any transactions or affect their reconciled status, you affect the Beginning Balance next time. Beginning Balance = the Net of all Previously Reconciled transactions. You can Ignore it and use the known Ending balance for that known Date from your source of reference, because the goal for any reconciliation is to end the Same. Ending Balance is always the Goal; the Beginning is a Reference, which has been affected, if you Recreated transactions. Example: I entered as checks what should have been Bill Payments, which I need to Change. I delete the Check and enter them as Bill Payment Checks, using original date and confirming I recreated with the Right same original amounts. Banking is Fine, but Cleared Status has been affected. I can use the Same most recent statement, its ending balance, and Re-Reconcile, clearing ONLY the recreated transactions that I know were previously Cleared. This is often called an Interim Reconciliation or "Mini-Rec."

Your goal is to Always have a difference of 0, so that you know you matched to the Ending balance.

"I am running QB 2012 - when I reconcile and click OK it does not ask me that question, it asks if I want to make a reconcile adjustment, which I do not."

Then you did not end In balance. You need to end with a difference of 0. Your ending balance from the statement is the goal and your Reference point.

"And when I go to just Write Checks, I can't seem to match up the credit card with the expenses."

You Don't Match anything. It is Just an Amount that you are paying against the Running Balance that you owe. This is a Micro-loan process. Every time you use the card, you Already Paid. There is no Paying of expenses after this. You used a card to pay. Someone Loaned you the money through the use of that card. Now you owe AMEX, or Visa, or whatever, a Running Balance of Increasing debt. You are paying down that Debt balance.

It is just One Amount. It is NOT an expense at all.

thank you - it took me a moment to process how to process the payments but I've got it now! Thanks.

"I cannot find a way to apply a payment made to the credit card"

On the Check, on the Expenses tab, the Credit Card is seen, and this is not an "expense" but paying down the balance of that card. If one check paid multiple cards, list them here and their allocation of the payment.

"I do not always pay the cards in full."

You don't have to; this process is a Balance Reduction process. You can see this in the Register view of the card accounts.