How do I research and verify my vendor 1099s either in anticipation of calculating and producing 1099s and/or in order to make adjustments?
There are three reports that are can cover all of your Vendor 1099 research needs.  They are located by menu item as such:
1.  Reports>Journals>Cash Journal> <1099 Detailed Vendor Total Report> and <1099 Summarized Vendor Totals Report>.
-This report allows you to audit and reconcile cash payments made to vendors.
2.  Reports>Lists>Vendor 1099 Adjustments> <1099 Adjustments>
-This report allows you to view system adjustments to vendors.
3.  Reports>Lists>Vendor Information> <Default &1099 Info-L>
-This report allows you to review vendors 1099 information.
How will the Cash Journal>1099 Detailed Vendor Total Report help when reconciling 1099s?
The Cash Journal is your best tool in reconciling vendor 1099s.  This report shows every transaction that was coded to the vendor and a cash account as well as its possible 1099 coding.
This report is located in Reports>Journals>Cash Journal. You will want to use the <1099 Detailed Vendor Total Report>.
This report includes the specific transaction entry activity that makes up the total by vendor and box number
I have a 1099 vendor and I’ve run a cash journal and the total for the vendor is ok but the amounts in the 1099 boxes are not. Why is that?
The most common cause of incorrect amount in a 1099 box number is because the vendor was not properly set up or the information not properly entered at the time of posting.
In order for a transaction to affect the value in a 1099 box it must meet the following three conditions:
1)    It must be coded to a CASH type GL account
2)    It must be coded to a vendor that at the time of entry was flagged as a 1099 vendor.
3)    In the data entry screen it must have a 1099 type associated with it and it must be coded to a 1099 box.
Many times a vendor will be initially set up and not all of the 1099 information will be available. Checks will be cut to this vendor and then later the 1099 information will be entered. The checks cut before the data was complete will not show in the 1099 box amounts, the checks cut afterward will.
This is most easily observed through a cash journal. You should choose the <1099 Detailed Vendor Total Report>.
With this report you can see not only the box total but the transactions that make up the total.  One change you will probably want to make to the default report is to change the column width on the 1099 Box to 0.75.  After that you will need to go to the Setup tab and type in a new Report Name (For example: 1099) before you can run it.
After you have run the report, take a look at the 1099 box number values. You can see transactions that were coded to the vendor but didn’t meet the criteria for being on the 1099.

I’ve checked my cash journal and the amounts still don’t agree to what is pulling into my 1099’s. What else am I missing?
Another source of 1099 values is the 1099 adjustments. These adjustments are done under Maintain>Vendors>1099 Information tab.
To get a list of adjustments go to Reports>Lists>Vendor 1099 Adjustments and use the <1099 Adjustments> default report.
Once I find that adjustments need to be made what is the easiest way to do them?
Go to Maintain>Vendors>1099 Information tab and there is a 1099 Adjustments form at the bottom of the page. Be aware that adjustments made in this fashion will NOT affect your financials statements or GL in any way. It will only modify your 1099 values. If you need to make adjustments to your financials and your 1099 information you will need to make cash type transactions that modify your 1099 amounts.

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