Payment Assignment

[Alun Champion]

Mac OSX, Gnucash 2.6

I'm trying to understand assignment of Payments to Invoices.
I've assigned Payments to Invoices 2 ways.
1) Process Payment (or Edit:Assign as Payment) -> Select Document
(Invoice). Result: Payment transaction + link lot transactions.
2) Process Payment (no invoice selected), View Lots -> Assign Lots
(scrub). Result: Payment transaction + no link lot transactions. It
looks like the Invoice is correctly assigned, as it doesn't appear for
the next payment.

So a couple of quick questions:
Are there any reasons for not doing it via option 2, which keeps the
A/R account much cleaner?
Why do the link-lot transactions not appear via option 2?

Cheers
   -A.