Visa officers don't care whether your salary is by cheque or bank transfer. But they do care if your salary is recorded rather than not recorded.

So if you paid your pay cheque into your bank account every week, then your pay amounts will show up in your bank account and they will be fine. Likewise if you kept all the paycheques and can send them to immigration, or if you kept your payslips for this period.

However if you took all those paycheques and turned them into cash, and don't have the payslips, then there will be no record of your pay and you will have trouble.