If you’re using a VPN tunnel to a non-Meraki client then you’d choose this under the IPSec configuration. For Phase 2 you’ll have to remove all other methods to ensure you are using SHA256. (Note: you need MX 15.12 or later).
For AutoVPN the white paper, https://meraki.cisco.com/lib/pdf/meraki_whitepaper_autovpn.pdf, states that it uses SHA256, but not sure how you’d verify this. Might be something support can verify, and ensure that only SHA256 is used.
