You can use Octopus Card or Airport Express ticket, group ticket or travel pass to enter the In-Town Check In area and check in your luggage. The Octopus fare is slightly cheaper than a single journey ticket if you are travelling alone and Octopus Card provides free MTR connection to Kowloon Station.
Officially, you are not allowed to disembark at Tsing Yi when travelling in the airport direction on the Airport Express. Instead, after checking in luggage at Kowloon Station take the MTR Tung Chung Line from Kowloon to its terminus at Tung Chung on Lantau.
If you don’t want to forfeit the fare for the Airport Express ticket you can take the Airport Express from Kowloon to Airport Station then take frequent bus fares S56 or S1 from the airport to Tung Chung, fare HK$3.5, journey time about 9 mins (S56) or 16 mins (S1). However this is less convenient and would take a little longer than taking MTR direct from Kowloon Station to Tung Chung.