Hi. We called them a few days after sending the application. They said if you've sent it through royal mail you can check it on their website. Then they sent us a letter asking for more documents and acknowledging what they've received. This is the same for your case. If they need more supporting documents, they will send you letter, if not, they probably won't.
As you said, they've deducted the money. It means they've received your application and it's under progress. Don't worry about the waiting time. It might take longer as they're very busy at this time.