You can't in the standard Sage 300 product.  A basic and long standing flaw.

I believe Tairox Productivity Suite can handle it (Tairox.com).

Thanks Stephen,

Do you know of any work rounds such as exporting the payment run and then re-importing? Or do you just have to pay for this add on?

I'm not aware of ant workarounds, sorry.  It would be nice if Sage addressed some of these gaps alongside some good work with new functions.

Sub MainSub()

Dim a4wLink As AccpacCOMAPI.AccpacDBLink
Set a4wLink = OpenDBLink(DBLINK_COMPANY, DBLINK_FLG_READWRITE)

Dim ApPaybatch As AccpacCOMAPI.AccpacView
Dim ApPayheader As AccpacCOMAPI.AccpacView
Dim ApPaydetail1 As AccpacCOMAPI.AccpacView
Dim ApPaydetail2 As AccpacCOMAPI.AccpacView
Dim ApPaydetail3 As AccpacCOMAPI.AccpacView
Dim ApPaydetail4 As AccpacCOMAPI.AccpacView
Dim ApPaydetail5 As AccpacCOMAPI.AccpacView
Dim ApPaydetail6 As AccpacCOMAPI.AccpacView

With a4wLink
.OpenView "AP0030", ApPaybatch
.OpenView "AP0031", ApPayheader
.OpenView "AP0033", ApPaydetail1
.OpenView "AP0034", ApPaydetail2
.OpenView "AP0032", ApPaydetail3
.OpenView "AP0048", ApPaydetail4
.OpenView "AP0170", ApPaydetail5
.OpenView "AP0406", ApPaydetail6

End With

ApPaybatch.Compose Array(ApPayheader)
ApPayheader.Compose Array(ApPaybatch, ApPaydetail3, ApPaydetail1, ApPaydetail6, ApPaydetail5)
ApPaydetail1.Compose Array(ApPayheader, ApPaydetail2, ApPaydetail4)
ApPaydetail2.Compose Array(ApPaydetail1)
ApPaydetail3.Compose Array(ApPayheader)
ApPaydetail4.Compose Array(ApPaybatch, ApPayheader, ApPaydetail3, ApPaydetail1, ApPaydetail2)
ApPaydetail5.Compose Array(ApPayheader)
ApPaydetail6.Compose Array(ApPayheader)

Dim sBatch As String

sBatch = InputBox("Enter the payment batch number:")
ApPaybatch.Browse "CNTBTCH = " & Val(sBatch), True
If ApPaybatch.Fetch Then
ApPaybatch.Fields("BATCHTYPE") = 1
ApPaybatch.Update
Else
MsgBox "Batch " & sBatch & " does not exist"
End If

End Sub

Thank you very much, that's great to know

Oh My Goodness!!!!! Thank you!!! 
However, I wish Sage would just change some programming and look for pending transactions, that's it, that's all they have to do, exclude pending transactions.  It shouldn't matter if a batch is a system generated payment batch, they should select all the criteria as given, ignore any pending transactions and allow the creation of the batch.

For anyone from Sage that might be reading this, this is an easy product feature / fix to add to an update and will save your clients thousands of hours of processing time a year.