When you start the Sage export you will see the following screen
The above screen allows you to 'synchronise' Onyx's data with any data you've already exported to Sage from previous systems. Most users probably won't need to use any of the functions on this screen, other than to select which export to run.
Where you've moved data from another system to Onyx, or you've been manually entering data into Sage rather than using this export feature, you might need to tell Onyx which records you've already exported, you do this by ticking the relevant record types (Sales Invoices, Purchase Invoices etc) and setting a data range for the records, then you select whether the records need to be marked as exported or not and then press 'Apply'.
So for example, if you've been using Onyx for a few years but not used the export feature, and you've been manually copying the data to Sage, you'll want to complete a manual export of records before a set data (say 15 June 2015), then you'll set the start date to some early date (perhaps even 1/1/1990 to ensure you get the earliest records), the end date to 15/6/15, select 'Mark as exported' and then press 'Apply.' Onyx will mark all records as if they've been exported and you can now start to use the export feature without any duplication.
If you've been using the export feature in Onyx V1 or V2 then payments were not previously exported. As they are now you'll want to avoid exporting all the payments that you've manually copied across (which would result in duplication), the easiest way might be to use the 'Mark payments for exported sales invoices as exported' button. When this button is pressed Onyx will find all exported invoices and then mark any linked payments as previously exported. The other button does the same but for purchase invoices.
Once you're happy to proceed, select the export you want to use by pressing either:
Transaction Export or Direct Export