For basic setups, you need 2 tools: a 6" steel rule and a Phillips head screwdriver.
Basic stuff is actually pretty easy. Don't be scared to adjust things, but err on the side of caution when moving your truss rod.
First off: Put some new strings on your guitar and stretch them properly.
How To Stretch Guitar Strings - Billy Penn 300guitars.com - YouTube
Next up is the neck. Fret a string (I use the low E) on the 2nd fret with your left hand, and then the 12th fret with your right pinky. That gives you a straight line to compare the neck against. Tap on the string between those points with your thumb (7th fret-ish) and the gap should be no more than the thickness of a business card on a high end guitar, thus indicating a very straight neck. If there's too much gap, tighten the truss rod very slightly. 1/4 turns translate to big movement. If it seems stuck, don't force it; take it to a shop. Tune between every adjustment.
Floating Bridge tension: If you have a floating bridge, it should be parallel with the body. If you're using the same gauge strings and the same tuning as your last setup, chances are your bridge is good to go. If you decided to go down a 1/2 step, your bridge is likely sagging into the body. Floating bridges are a balance between string tension and spring tension. If your bridge is sagging, loosen the springs in the back, retune and check it again. If it's way up in the air, tighten the springs, retune and check it again. This can take awhile if the bridge is way out of whack.
String Height: This is also known as action and is always always always adjusted at the bridge. Depending on your guitar, you'll either have a 1 piece (tune-o-matic style) or individual adjustable saddles. The tune-o-matics are dead simple. Use your steel rule to measure the top of the 12th fret to the bottom of the low E string. The factory specs for your guitar are likely published on the manufacturers websites. My guitars are approx 1-2mm off the top of my head. Use the thumb wheels to adjust each side up or down. Tune between every adjustment.
If your guitar has individual saddles, you'll need to not only set your height, but make sure you measure each string string so that the radius of the saddles matches the radius of the fretboard. Stew-mac makes an "understring radius guide" for this, which is pretty helpful, but not necessary.
Setting relief: It's back to the neck looking for buzz. Play your guitar. If you have buzz from open strings to frets the 5th fret, but nothing after that, you need more bow in the neck. If you buzz from the 5th fret to the 12th fret, you have too much bow in the neck. After each adjustment, tune and check your string height.
Intonation: This should be the final step as almost every other adjustment can affect it. Your 12th fret is exactly the midpoint between your nut and bridge, which is why the harmonic is an octave of the open string. Tune to your 12th fret harmonic. Now, fret the 12th fret and see if it's in tune. If the fretted note is flat, that means the length from the 12th fret to the bridge is longer than the length between the open string and the 12th fret. So, you need to shorten that length. If the fretted note is sharp, you need to lengthen the string. Your bridge has screws that move the saddles back and forth, use these to adjust this length.
You're done! That's a basic setup.