I am about to complete my 1st end of month on sage instant, In manual bookkeeping I have always made an adjustments for Cheques written ie. September but issued in October. I wanted to confirm the when I use the reconcile bank account and leave them as unreconciled this will make the adjustment for me (if this makes sence?).
When you do the bank reconciliation at month end, if you leave unreconciled the cheques that have been written out but not presented at the bank yet, then they will stay on there until the following month. This has the same effect as doing a manual bank rec.... i.e. Bank balance - add un-presented deposits - less un-presented cheques = cash book/Sage balance. Sage won't make an adjustment for you as such, but if, after matching all your bank items in the reconciliation window there is a difference in the "difference" box then there is a problem somewhere and you need to find the error.
To be honest I always do a manual bank reconciliation in Excel as well, just to make sure they match.