Underseal

First you need to chip back the rubber underseal to ensure it is all sound .. what tends to happen is that once water penetrates then it creeps/rusts up behind the rubber.. so make sure you have paint with no rust or it will keep on failing. I tend to use a big old screwdriver.. but then go overboard often with welding chipping hammer, cold chisel and light 12oz hammer, air powered needle gun :shock: .. but there is no weak metal left!..

Then repair paint..
Industrial hot pressure washer .. preferably up in air
Dry dehumidified shed..
power wire brush on 4-4.5" angle grinder (knotted/twisted brushes only),
hand wire brush and blunt screwdriver to get mud out
chipping hammer from your welding set for mill scale :shock:
neutralise with Fe-1-2-3 http://www.rust.co.uk/rust-converters.cfm,
Zinc rich paint http://www.bilthamber.com/electroxbuy.php
top coat of say Hammerite but Rust Bullet would be even better (but expensive),http://rustbullet.com/links.htm
waxy top coat Dintrol 4941 http://www.rust.co.uk/dinitrol-products.cfm ..

I used to use the Waxoyl loaded underseal .. but all underseal has this issue with creeping rust/water.. the real trick is in getting a continous unbroken coating which means spraying to me and hence Schultz gun cartridges and Dinotrol is the more professional version of Waxoyl .. it will stop a bit but expect it to fall off in 18-24mths with more rust if you do not paint first..