You can place the weapons you wish, in the numbers and combinations as seen fit. Of course a weapon will take away space (which is limited on each type of hull) and you will want to add defence systems or additional engines, etc.
There are 3 basic weapon (and corresponding defensive system) categories: Missiles, Beam, and Mass drivers.
Missiles = Self explanatory
Beam = Everything from Lasers, over Plasma, Phasors, etc
Mass drivers = Basicaly what we have today- bullets
Defensive systems protect against particular weapons only: I.e. Against Mass driver weapons you will need to armor your ship, while against missiles only anti-missile chaff systems will be effective. Against beam weapons Force field Shields are the defence.
Engines= There exist a number of engines, all in the same linear branch of the tech tree. You start with bulky and slow stuff and the more you ressearch the smaller and faster they become.
Its not always useful to upgrade a ship design straight away, i.e. with every little new technology researched. Often new technology frees a few space limit points but thats merely it. The higher up the research tree you get, the greater the benefits per new technology.
Note: There exists a different tech tree branch called "miniaturization". Sticking to this one won't make your ship engines faster, weapons better or your defence more effective, but you'll may be able to fit more of a certain type of system on your ship.