yeap very trival todo, you use the bonded-interface name in your vlan-subintf
 
 i.e here' s one of  my 620 connected to a Nexus
 
 
 
 config system interface
     edit " bond0" 
         set vdom " root" 
         set type aggregate
         set member " port1"  " port2"              
         set alias " bonded to nexus 7K " 
         set algorithm L3
     next
 end
 
 edit " vlan-DC01-SW1" 
         set vdom " root" 
         set ip 172.16.199.11 255.255.255.0
        set interface " bond0" 
         set vlanid 178
     next
 edit " vlan-DC01-SW21" 
         set vdom " root" 
         set ip 10.11.0.11 255.255.255.0
        set interface " bond0"       
         set vlanid 888
     next
 edit " vlan-DC01-SW31" 
         set vdom " root" 
         set ip 172.16.88.11 255.255.255.0
        set interface " bond0"  
         set vlanid 23
     next
 end
 
 
 
 Just adjust the switch and FGT for the load-balance algorithm to achieve your desired balance.