the trick to not getting water in your shoes is stopping the water coming in from the cuff and also from underneath, as well as the overshoes themselves. But understand, nothing, if given enough time will remain 100% waterproof. So being warm and relatively dry is your best bet, as you will get wet.
It starts at the body, no water down the neck, back or legs means it wont trickle into the shoe. So waterproof helmet cover/hood/hat and then a waterproof jacket (the pros swear by the castelli gabba). Also look at either waterproof or neoprene gloves for your hands.
Then for example, castelli nanoflex tights are good at stopping mild to decent rain from getting in, if you then put the cuffs of the tights over the overshoes then water shouldn't get in the overshoes. Some people use sealskinz socks to stop water getting to your feet but there are some varied reports, YMMV.
As far as underneath water entry is concerned, plastic bags and tape can cover entry parts on your shoes, keeping mind your feet wont be able to breath, so they might get wet from sweat on the inside. Failing that, true waterproof or winter shoes can help.
http://road.cc/content/review/104965-no ... -gtx-shoes" onclick="window.open(this.href);return false;
here's some light reading, about waterproof gear and overshoe reccomendations:
http://singletrackworld.com/forum/topic ... -overshoes" onclick="window.open(this.href);return false;
http://www.bikeradar.com/au/gear/articl ... oes-35721/" onclick="window.open(this.href);return false;
http://road.cc/content/buyers-guide/788 ... g-clothing" onclick="window.open(this.href);return false;
http://www.bikeradar.com/au/gear/articl ... ing-35713/" onclick="window.open(this.href);return false;
http://www.bikeradar.com/gear/article/b ... ing-36023/" onclick="window.open(this.href);return false;
http://road.cc/content/buyers-guide/672 ... essentials" onclick="window.open(this.href);return false;