Hi, there are many solution to gather a proof of online payment. I believe you might be aware about the "print screen" option available on your key pad. With every proceeding step, you can take a snap of your screen by pressing "fn"+ "prt sc" and save that to word or paints. In that case you will be having a record in case some thing goes wrong. You can also grab the error page, if any, to claim your payment. But rest assured, it has been devised after so many trials with every possible efforts to minimize any problem.
And if you still dont feel comfortable, there is no such problem with the banks. You can consolidate your heat by saying that when I can wait for months-years for the out come of application, will have to add merely a few days for fee deposit by banks.
Best Wishes,