When designing a ship, I have a pretty simple process. First I ask myself what the primary role of the ship should be. Something specific. "Warship" isn't specific enough. "Missile cruiser" is better. "Point Defence Ship" is better. Once I've got the primary role sorted out, then, before I design even a single component, I decide how much of the total size I want to dedicate to engines. As a rule of thumb, I've found 20-25% is a good standard for reasonable speed. So, for example, a 10,000 ton military ship would then have 2,500 (25%) tons to dedicate to engines. Since redundancy is good for military ships, I'd probably break that down into either 2 size 25 engines (1,250 tonnes each) or 5 size 10 engines (500 tonnes each.) You could do 3 size 16 or 4 size 12, but you wouldn't come out to exactly 25% engines that way (which could be fine, as long as you're close enough to your goal.)
Once engines are sorted out, then I tack on the one-off systems that I know I'll want on just about every ship. Damage control and emergency cryo transports are the only "must-haves" on that list, anything else is up in the air.
Then I pack as many systems onto the ship as possible which fulfill its primary purpose. For missile boats, that means launchers + magazines. For point defence, that usually means turrets or AMM launchers + magazines. Just pack as much on as you can without going over your target size.
Then, with whatever is left, I'll add defenses. Armor and shields, until I get as close to the target size (without going over) as I possibly can.
Once all that's done, it's time to tweak. The big things you'll be looking to tweak are maintenance (via engineering spaces), deployment time, and range (via adjusting fuel tanks.) Remove whatever you think you can spare in order to ensure you've got the desired maintenance, deployment time, and range.
Once all that's done you should have a ship that has a clear purpose and everything it needs to accomplish its purpose.