Each payment has a single thank you letter, even split payments will generate a single thank-you letter.
When splitting a payment, if using the Built-in letters, the purpose field will display "Multiple" if more than one subcategory was used.
Word Merges have a field for <SplitDetail> which can be used to display the details of the split.
If only part of the payment is tax deductible, the Goods and Goods Value should be entered. Click the "..." button next to the Amount field to enter this info.
This Goods Received details will automatically come up in the built-in letters. Word Merges should use those specific fields for <Goods>, <GoodsValue> and <TaxDeductableAmount>.
In Kind Letters separation
Because of this change in the way letters are generated, batch thank-you letters will no longer include In-Kind donations letters in the same batch. These need to be done in a separate batch.
This was done due to the major changes to the way letters were being generated, namely the combining of splits into a single letter. In Kind letters don't use the Amount field and should not be split.