Ok thanks, I tried with 'local" before and got very bad results, did some digging and turns out that was because I was having the same driftfile on both instance (probably the parameter isn't necessary on the server config), it's better now.
I specified a custom sock as bindcmdaddress for each instance (/var/run/chrony/chronyd_1.sock and /var/run/chrony/chronyd_1.sock) and a custom cmdport for sthe server instance.
I can get chronyc to work with both instance, however ntpdata is not working on neitheir of them, i get "501 Not authorised", any idea ?