Hi Chetan,
You might be having a BOM that uses the SFG to get the FG.
The process that you described is that you simultaneously manufacture two SFG.
and ur challenge is that- when the FG is to be manufactured the system wont allow you to process the Order as there are not SFG in stock. I hope this is correct.
If so, then as Davinder mentioned, you need to keep the issue method to Backflush for both SFG so that when the SFG's manufacturing is completed the inventory in the ware house will automatically updated, so while manufacturing FG you will not run out of Stocks.
Also If it is on manual then complete the production for SFG, take the goods receipt into the warehouse so that you have the required quantities to start the production of FG.
So for you to automate and minimize the intervention, you need to make the Issue methods to Backuflush (This needs to be done at the BOM), this will automatically update the quantities as soon as you complete the process.
regards,
Ravi.