First rule of survival in a sword fight: keep the "Block" key pressed, wait for the enemy to try to hit you, then immediately hit him back - he's just swung at you so won't be ready to swing again, and he's just swung at you so his block is down. Watch for him to flinch - if he does, hit him again. Otherwise press "Block" again, keep it pressed, wait for the enemy to try to hit you...
Don't let your officers into fight until their Melee skill is at least 4 and you've given them a decent weapon, and preferably armour. You can talk to your officer, go down the list of answers to "About you", then say "Why don't you sit out the next boarding". When he's ready you can use the same procedure to tell him "Next boarding, you're coming with me".
If you're playing the standard storyline ("Tales of a Sea Hawk"), get yourself a good reputation and then go to the tavern in Kralendijk, Bonaire - there's a chap sitting just to the right of the door with a problem which he'll tell you about if you're a decent type, and the reward for helping him is one of the best swords in the game. Otherwise go on a dungeon crawl. Save often in case you get killed, but when you're low level, so are the enemies, making them easier to beat. And you'll probably find a decent sword lying around somewhere.
Shooting your people doesn't do any harm apart from wasting a shot - friendly fire doesn't do much damage. I'd have thought a grapeshot pistol which hits everyone in front of you would be a good thing as your men don't take damage but enemies do. However, I don't often carry one so I can't speak from personal experience. A single shot pistol probably will hit the nearest person in your line of sight - these are primitive pistols with no gunsights so precise aiming is not an option!