Our suggestion for entering stock is to enter it as Cash with the amount it was sold for (if sold on the same day) or according to IRS Publication 561, "Determining the Value of Donated Property" (bottom of page 5), the fair market value of donated shares is the average price between the highest and lowest quoted selling prices on the valuation date as the Amount (as that is what you would receipt the Donor for and what they would claim on their tax return).

If you want to reference the fact that the gift was OF STOCK in your letter/email, what I would suggest is adding a description of the gift to the Note (e.g., "99 shares of ABC Corporation") that you could drop into the letter. Since there is no field for Stock you might consider creating a Transaction custom field that you could filter Stock gifts with. You could make the field vague or specific depending on your personal preferences (as broad as "Additional Payment Types" with Stock being a single (perhaps initially only) option or as narrow as "Stock Gift" with just the option of "Yes").