New company bank account setup plus the sort sequence when reconciling.

I know this issue has been addressed many times  but I am confused and need clarification.  I have a very large active company, with an equally active bank account that needs to be set up.  Due the the excessive outstanding checks and debit charges, I lumped them all into one figure because we could not tell which ones were going to clear and which weren't.  Many checks were voided and no record of the void was made.  

I am now trying to reconcile from Jan09 to Dec09.  There are hundreds of entries almost every month.  I understand that I need to enter the known outstanding checks, and the known debit charges (which I have now ascertained) but I am still unsure as to how and where I set up the beginning balance.  I was going to do it by journal entry but one of the instructions stated that I should enter the bank's ending balance in the reconciliation form.    Any help you can give will be appreciated.

I also have another issue.  With hundreds of entries for the year to reconcile, how can I get the reconciliation form to sort the checks, EFT's, ATM's, etc by Date?  I have tried and tried with no results.  I even called support and we couldn't get it to sort.  It will sort by date within a number range.  (Explanation:  I use an alpha for each person with a debit card because our bank post entries for debit cards separated by card # - So if all D's are sorted by that alpha then sorted by date- It is difficult to bounce between all the alpha's to search for one certain entry.  I would rather it sort by the date, then the alpha or #.  This is a really big issue so if anyone can help I would so appreciate it.