Unfortunately, GoDaddy Bookkeeping does not currently offer reconciliation functionality. This is a popular feature request and we invite you to make your voice heard and add your support for this feature request here: http://help.bookkeeping.godaddy.com/entries/21207802-reconciliation.
In the meantime, here is a workaround that you may wish to use:
You can reconcile certain things in GoDaddy Bookkeeping. You can reconcile your fees, and sales, though we do not distinguish sales by importer. This is why we no longer call sales eBay sales, but now refer to them as sales. As we have increased the # of companies we import from, we have found it necessary to switch from distinguishing sales by company to the more general sales. You can get monthly totals though for most vendors and/or categories. To do this, please follow the instructions below.
Starting on Overview page:
1. click on the appropriate ledger (Income/Expenses)
2. let the page load
3. adjust date range to desired time/dates
4. adjust the remaining fields accordingly (you can search by account, payee, and or category)
5. click filter.
For example, let's say you want to reconcile your eBay fees for June of 2012:
1. click on the expense tab
2. adjust the date range from 6/1/2012 to 6/30/2012
3. change All accounts to "eBay Seller Account"
a. you may also change Payee to "eBay"
b. change category to "eBay Fees"
4. click filter
the # above the ledger on the right side is the total $ amount for the chosen period. You can also check the # of transactions by scrolling to the bottom of the page where you will see "viewing ## of ### transactions." This is the total # for the month.