Yes, you can just set your Data connection to only your 2nd Sim.
Then all the 3G data flow (be it in Whatsapp, LINE, Skype, browser, youtube etc.) will be through your 2nd Sim unlimited data.
I used my Redmi this way for 10 days :
Slot 1 : Sim with Mobile Data Plan 500MB/month free with my recent sign up of Fibre Optics broadband (no voice and no sms capability but has a phone number starting with 9 too).
Slot 2 : Sim with normal Mobile plan (Voice and SMS) number 9xxx which I use to register for my Whatsapp and LINE.
I set my Data connection only to my Sim 1 (i.e. the Sim with mobile data 500MB/month). (There is an option in the setting of which Sim you want the default data connection to be).
When I double checkd on my data usage for the 2 sim on Singtel website, it showed zero MB for the phone number of my Sim 2 (voice plan) and apparently all the data flowed through the phone number of my Sim 1 (mobile data).