When you say "running Document merge" are you referring to the menu item Actions >> Document Merge? If you are, please be aware that the Actions >> Document Merge capability is exclusively used to process Merge Documents that present data from one or more Contact records. It cannot be used for anyother type of merge document. The only place a Quote merge document can be created is from the Reports tab of an open quote. Of course it can also be printed 'automatically' when selling a quote.