Doubts on manufacturing

We issue goods for manufacturing our product,but actual quantities used for the manufacturing are known only after the servicemen return to the company.

Now we are doing the production order like this
1.create bom with materials(not actual quantity)
2.submit production order
3.Transfer material for manufacture
4.If any material is returned.create a stock entry manually with purpose transfer,and will transfer the excess material from work in progress ware house to store
it working fine in this case

but when we need to use some extra material after submission of production order and material transfer for manucture stock entry,we dont know what to do

Also we are not using operations in BOM.All operations are managed using project and it ok to use manufacturing module without operations

please help

You should be able to do this with average quantities atleast. Also when you backflush (finish) the Production Order, you can add / edit quantities based on the exact number.

Not doing operations via ERPNext is fine, you may want to account them to COGS at some point (again depends).