We just added an additional way to record a gift of stock as a special type of Gift-in-Kind. This allows you to record this donation with a dollar amount (after you sell the stock). The gift displays in the Gifts-in-Kind section of the contribution statement, but the amount does not display. However, because there is an amount associated with it, that amount will be applied toward any pledge to the same fund.
In addition to this new contribution and bundle type named Stock, there are other ways you can record stock. One way is to record it first as a Gift-in-Kind at the time of the donation (with no dollar amount) and then as a Non-Tax-Deductible gift after you sell it (with a dollar amount).
The method you choose will depend on several other factors, such as whether you display non-tax-deductible items on the giving statement and whether or not the gift should be applied toward a pledge.
Just be sure to check out the help articles relating to this, so that you make the best decision for your church and your donors.