Use of Production Orders for Non-BOM items

Dear All,

I don’t know how to put these thoughts on paper, but I would any how give it a try and I have done a number of times before but I guess my thought conversion into the words is not so precise or may be what I am asking for is too much.

We are basically making tools and here we don’t use any BOM for Raw Material to finished goods due to various reasons.Now how do we track the production, is through various warehouses. We have different warehouses for different kinds of processes, now the thing is that once the material is taken into production we track the quantity of that material in different warehouses and then once the process is completed we transfer the material via a stock entry to another warehouse.

Now the problem is not for material in production but for items which are needed to be taken into production, aka, Production Order.
Now currently the system would not allow us to make a stock entry for a production order where as the system calls it we could backflush the quantity and make the Production order pending as ZERO.

Is it possible to make a Production Order for Item A which does not have any BOM and then make a stock entry where we receive ITEM A in one warehouse and consume the RM used in making Item A from another warehouse.

Currently we are tracking our production orders via Google Spreadsheets which any one would say is not the best way of doing things right but it is a makeshift arrangement.

Any help in this regards would be highly appreciated.