Hi @sme
Selling from stock during your trading year is generally done from the General Purchase (5000) nominal code, and the stock codes themselves come into play at year end (there are a few topics on the forums about this - a quick search should bring up a few)
Normally you would just raise a sales invoice as normal, and use one of the sales nominal codes such as General Sales. In your profit and loss report this will then be shown as income, whereas General Purchases will be shown as expenditure.
Any sales or purchase invoice or estimate can be assigned a project tag. However, you can only do it as an invoice as a whole. Although you may this is a bit tricky (given that you probably bought more stock in one purchase invoice than what you sold in one sales invoice), you can use project adjustments.
There’s a detailed guide on the project tags, here, which also includes adjustments.
Please let us know if you need any further help.