Once you have confirmed that you have properly run the FACTS to GL Comparison report ( see I would like to understand how to run the FACTS to GL Comparison Report), then you should also do some analysis as to what caused the problem.  See What did I do to cause the FACTS to GL comparison report variances? to help troubleshoot the issue.  Before fixing the problem you should try to determine the cause and fix it by correctly undoing what was done wrong.

If the problem can't be determined, but you are certain that either the FACTS value or the GL value is correct, then fixing the variance is easily accomplished.  Note that complementary variances ( one positive in one fund and a negative in another fund) are typically caused by attempts to close funds out of the pool incorrectly.

Once you have determined which value is correct:

If the FACTS balance is correct and the GL is wrong, then make a journal entry to correct the GL balance and use an FA journal key.  Journals with an FA key will not post back into FACTS and thus won't change the FACTS balance, but will change the GL balance. Note that journals made will typically include the pool asset account and a revenue account ( typically unrealized gain).

If the FACTS balance is not correct and the GL IS correct:
  1. Go to the Pools tab in FACTS
  2. Find the Pool and uncheck the prevent manual transactions box.
  3. Go to the Reconciliation tab and then the Transaction tab
  4. Click New
  5. Enter in a new FACTS transaction.
  6. Use mscp for the type and fill in the rest of the information.  The amount should be the variance.
  7. After entering in the transaction(s), rerun the FACTS to GL comparison report.  
  8. If created correctly, the variances will disappear.
  9. Repeat step #2 and recheck the box.
Note that this WILL cause the pool balance to change by the net amount of these new transactions.  Depending upon the value, the only way to get FACTS to balance will be to adjust the unrealized value for the current cycle by the total of the transactions. In many cases the variances net to $0, but the individual funds are out of balance.  Thus creating these transactions that net to $0 will not impact the total pool balance.