Q: how do you command multiple units at once? I have like 20 battleships and I want to use them together to attack.
A: You can't; not in Civ2-you have to send each unit in separately and they each attack individually, not as a team
You can do this in Civ3 with the use of Armies, but i've never done that. Civ CTP had this option as well I think, but that game just sucked all around
Q: why can't I take cities with my battleships? I have taken out defences in like 50 cities now, but I can't take them over, it says that you can't take cities with ships, but I don't really use land units except for defending, they die way too fast.
A: You can't take over cities with your boats. If you don't like ground units, then take over the cities with Helicopters. But in their defense, ground units can be useful in protecting captured cities-whether you like Riflemen, Alpine Troops, Mechanized Infantry or Marines is up to you. At some point in the game I like to defend with Stealth Fighters. But you still need to take over cities and that's usually done with ground units. I prefer Armor units for their movement and strength.
Q: what is better to use, nuke or cruise missles? they cost about the same, but the nuke does a heck more damage.
A: it's not really a matter of cost but rather of what you're trying to accomplish. If it's just basic destruction of units then your Cruise Missiles can get the job done. Nukes are useful to conquer well-defended cities. Nukes cause pollution and all nations get really pissed off at you-if you use Nukes, be prepared to defend yourself against everybody. This is not really important if you're down to a final war between you and 1 remaining civ, or if you are much stronger than your other opponents.
Nukes can also be useful in taking out enemy navies if they bunch their units too close together (which the AI always seems to do). As an added benefit, there is no pollution in ocean squares so you don't have to worry about global warming when using nukes in the middle of the ocean.
Personally I don't use either type of missile; they're too expensive and you can only use them once before they're destroyed. I'd rather use an armor or horwitzer which is very strong and can live to fight another day. The only time i'll build nukes is as a deterrant; if you have nukes built and nobody else does, your enemies will be more likely to ask for peace. I'll do this when i want to go to space and don't want to worry about war.