There is nothing to stop you raising sales invoices in the business name of JS Associates but you have to consider those customers who pay by cheque – who they would make payment to?
If you have set up your bank account as ‘John Smith Trading as JS Associates’, your bank will accept their cheque made out to JS Associates for credit to the business bank account. If not you could still invoice as JS Associates but you should put on the invoice in a prominent position “Cheques should be made payable to John Smith”.
Once you settle on a style for use you should continue with that style so, for example, if you subsequently register for VAT make sure that the registered trader is in the same style.