My passport also expired.
Then you shall get a waiting number, to submit everything at Counter 3, the officer will take a digital photo of you That will be your passport photo, make sure you wear dark colour clothing, or they will borrow you a dark jacket to cover up.
As for most of the communications with the Malaysian Administration, you may do it yourself, however the process can be time-consuming and there are good consultants familiar with how to present your case and ensure a speedy approval from the Authorities, It generally takes between 3 to 6 weeks to get the status and work permit approved.