The peasant armies of Joseon at the time of the Imjin War were poorly armed compared to the well-paid feudal troops of Japan, most of them usually going into battle wearing rudimentary cloth-and-cotton armors and farming equipments, or at best, tridents. But Joseon had a huge superiority over Japan at the time in the sea, and one of the most remarkable and ingenious naval weapons that Joseon had in its disposal was the Geobukson, or the 'turtle ship', which was the first iron-clad warship to have fought a naval battle in history. The ship had a low deck and mast profile which made it easier to dodge cannon shots, and the iron-clad deck could sustain full cannon shots, as well as impede boarding attempts. Japan achieved terrifying success against the 'ragtag' armies of Joseon in numerous land battles (Joseon was very poor in cavalry, and had no muskets for the infantry, only cannons), but Joseon achieved similarly terrifying success against the ragtag navies of Japan in naval battles. Because Joseon was able to maintain credible sea superiority over Japan through the most of the war, Japan was never able to successfully establish a stable supply line to support its land invasion force, which was one of the big reasons for the downfall of Japan's invasion efforts despite Japan having outnumbered the combined Joseon and Ming army in the Korean peninsula by nearly three to one.
Here are the best sourced wikipedia articles with regard to significant naval battles in the Imjin war:
http://en.wikipedia.org/wiki/Battle_of_Hansan_Island
http://en.wikipedia.org/wiki/Battle_of_Myeongnyang
You can see here how the peasant soldiers/marines of Korea were armed during the time. The lieutenants usually wore hardened studded lether armor, and generals wore more sophisticated scale armors. Tridents and bow were the most common weapons of choice of the Joseon infantry, while the Japanese infantry often used muskets and shortswords. Swords were usually reserved for officers and commanders only in Korea.
http://www.youtube.com/watch?v=NzkT-kg01is
This is the trailer of a drama episode that reenacts the final naval battle of the Imjin War, the battle of Noryang; it was perhaps most fierce naval battle fought in the entire war that had seen participation of all the three belligerents, and it's also where the Korean naval strategic mastermind Yi Sunshin fell, although the battle was still won on Yi's side. Allow it to help you imagine how the naval battles in the war would have played out.
http://www.youtube.com/watch?v=v0NWbcqYbVo
Korea was historically one of the world's most accomplished masters of seamanship and shipbuilding. Korean seamen and ships could sail and fight in treacherous waters that their Japanese or Chinese counterparts could not, and apparently, that unprecedented historic reputation of Korean naval dominance in the relevant parts of the world lingers up to the modern day, if Korea's present domination of world shipbuilding is any indication. You should balance Korea and Japan's military by giving Korea superb navy but relatively poor army, and vice versa for Japan.
http://en.wikipedia.org/wiki/Shipbuilding#World_shipbuilding_industry_in_the_21st_century