I'm extracting invoice data from quickbooks 2005  from the "Invoice" (Header) and "InvoiceLine" (Line Items) tables. Inside quickbooks an invoice shows as paid, but in the "Invoice" data from the extraction the "IsPaid" field shows False. However, in the "InvoiceLines" data the items for the same invoice show "IsPaid" as true. Can somebody explain to me how I would go about reading this data and determing if it's actually been paid or not?

First of all, you don't normally need to link InvoiceLine to Invoice because InvoiceLine contains most of the information in the Invoice header anyway. But to prove my point, and address your point, I ran the following queries:

SELECT InvoiceLine.TxnID, InvoiceLine.invoiceLineTxnLineID, Invoice.TxnID,
InvoiceLine.IsPaid, Invoice.IsPaid 
FROM InvoiceLine, Invoice
where InvoiceLine.TxnID = Invoice.TxnID

Results 917 Rows

SELECT InvoiceLine.TxnID, InvoiceLine.invoiceLineTxnLineID, Invoice.TxnID,
InvoiceLine.IsPaid, Invoice.IsPaid 
FROM InvoiceLine, Invoice
where InvoiceLine.TxnID = Invoice.TxnID
and InvoiceLine.IsPaid <> Invoice.IsPaid

Results 0 Rows

There were no differences found. I suggest you run this on your system too! If there are results, try this instead:

SELECT InvoiceLine.TxnID, InvoiceLine.invoiceLineTxnLineID, Invoice.TxnID,
InvoiceLine.IsPaid, Invoice.IsPaid 
FROM InvoiceLine, Invoice Unoptimized
where InvoiceLine.TxnID = Invoice.TxnID
and InvoiceLine.IsPaid <> Invoice.IsPaid

If there only 0 results using the Unoptimized tag, then you will need to resync you optimized tables by doing:

sp_optimizefullsync InvoiceLine

and

sp_optimizefullsync Invoice