I would try exactly what you already suggested. Do the whole /ip nat mangle for the next in-interface. Though I will admit I have never tried this I have no reason to believe it wouldn’t work.
/ ip firewall mangle
add chain=prerouting in-interface=LAN1 connection-state=new nth=1,1,0 \
action=mark-connection new-connection-mark=odd passthrough=yes comment="" \
disabled=no
add chain=prerouting in-interface=LAN1 connection-mark=odd action=mark-routing \
new-routing-mark=odd passthrough=no comment="" disabled=no
add chain=prerouting in-interface=LAN1 connection-state=new nth=1,1,1 \
action=mark-connection new-connection-mark=even passthrough=yes comment="" \
disabled=no
add chain=prerouting in-interface=LAN1 connection-mark=even action
/ ip firewall mangle
add chain=prerouting in-interface=LAN2 connection-state=new nth=1,1,0 \
action=mark-connection new-connection-mark=odd passthrough=yes comment="" \
disabled=no
add chain=prerouting in-interface=LAN2 connection-mark=odd action=mark-routing \
new-routing-mark=odd passthrough=no comment="" disabled=no
add chain=prerouting in-interface=LAN2 connection-state=new nth=1,1,1 \
action=mark-connection new-connection-mark=even passthrough=yes comment="" \
disabled=no
add chain=prerouting in-interface=LAN2 connection-mark=even action
Trying to get src-nat and dst-nat with load balancing is a trick I haven’t been able to figure out though http://forum.mikrotik.com/t/multiple-wan-gateways-with-src-and-dst-nat/10557/1 The outbound stuff passing through the router works pretty well but I ultimately switched back to WRAP w/ Debian.