Hi Pascal
First of all, upgrade EEM/WCC to 11.4 SP6 because WCC 11.4 SP4 cannot manage Autosys 11.3.6 SP7
This WCC Service Pack can also manage your 11.3.6 SP5 instances.
1) When done, you can upgrade one Autosys instance at a time.
2) If this is an HA environment with a single database, you'll have to upgrade both schedulers/application servers because the scheduler and application server code must match with the database schema
3) If this is an HA with Dual Server environment ( two databases ) you'll have to update the 3 machines and both databases
4) If WCC is in HA mode (which means with a single and common database), both WCC servers must be down before starting the WCC upgrade (and indeed, update both WCC servers)
Regards
Jean Paul