Create a liability account called gift certificates
create a service item named gift cert and link it to the liability account
use that item on customer credit memo when you issue the GC
when they buy something and pay for it with the GC, list what they buy, and apply the customer credit
Journal entries should be the exception when using QB, they often do not work as you think they should, and when you use inventory type items they never work for inventory. It is much better to use the forms on the home page the way QB is designed to be used. Journal entries also bypass accrual/cash reporting, and will not show on many reports.