From what i remember the money is taken fairly early on as i remember on another website them mentioning that if a Cheque was used this meant it took them longer to start the process and could give an extra day or two to someones application if needed.
When we applied for ILR in person the fee was taken just after a basic check of the documents but before the application was processed. Before we were interviewed a quick note of our receipt was taken to say we had paid by the interviewer very quickly done.
This is to stop people I guess putting applications with out the right funds available.
But as Terpe says if you do not have a letter of acknowledgment it may well be worth checking the status of the application.
If unsure best to place spare money in just to be certain.
I hope you receive some good news very soon regarding your FLR
