Archers? I'm assuming you mean some type of infantry or cavalry. Anyway, during combat, units form two rows. Each row has a width called your "combat width", and each unit takes up one square on this little grid. Infantry should be the bulk of your army: It sits in the front line and attacks regularly (and blocks the back row). Cavalry sits off to the side of the infantry and flanks. It has high shock damage, but low fire damage (basically the two phases of combat; shock is more important early on, then fire starts going when artillery becomes viable around military tech 13). Artillery sits in the back, although it can fight from the front; however, it is very expensive to reinforce and thus it should be in the back at all times if possible.
Yeah you can't take cities using ships. If two navies that aren't both transporting armies (although they might have fixed that bug) run into each other, they'll fight. Light ships help raise your trade power in a node. Blockades get you more money, lower the amount of money the foe makes, give war score, increase the war exhaustion of the blockaded country, and make it easier to siege any blockaded provinces.
Not necessarily. A good way to stop rebellions is to raise autonomy. While it will become significantly less likely to rebel if it's your religion and an accepted culture, it's still possible. A country disunified in religion has increased cost for extra stability and increased unrest all around.
There are three categories of missions, and every mission has a weight. This weight is modified by various factors, and some factors can disable the mission altogether. Whatever mission has the highest weight in each category is the one that is shown.
Piety is a function only for Muslim nations. High piety makes your armies fight better, increases the time your foes take to siege your forts, and increases the strength of your missionaries. Low piety makes you get cheaper tech, gives you more manpower, and increases the amount of tax you get. Generally, you want to either keep this as low as possible or as high as possible.
Don't be afraid to fuck up. If you do fuck up, don't call it a loss.