Inventory items gl accounts always override customers gl accounts. If you are selling stock or assemblies items I would not advise you to add multiple items for the same item because you will constantly need to make inventory adjustments for quantities you sold but did not have for that particular item. You would not have the issue selling non stock items but then you would not ever know your quantities on hand, etc etc. 

when invoicing just change the gl account to the correct one. To display the gl accounts on the SO screen go to options on the top menu bar, under the accounts tab uncheck hide gl accounts for Account Receivable.