bitcoin payment processing, using bitcoin uri I am interested in processing bitcoin payments in my application.
I read about bitcoin uri, but its unclear to me how to match the payment transaction to a specific 'user id' in my application? 
Is it possible to include the 'user id' on the tx? is it recommended?
You should manage this in your app by generating a new bitcoin address for each payment from each customer, so that if BTC is received on a specific address, you know what it is for. This keeps specific transaction data private internally in your application rather than public on the blockchain too.