Do they both act on the same routing tables ?
There is for all purposes just one routing table which the kernel maintains and you manipulate that using the route command (generally). There is also the ip command available. But both act on the same routing table.
iptables is best thought as a filtering and packet mangling utility which happens before/after routing and as such can affect the routing decisions overall, but no, it does not manipulate the kernel's routing table.
-- Rohan http://rohan.almeida.in