The neck must be fastened to the body before you are going to position any bridge. An important factor that determines where the bridge will be situated on the body is the point where the neck meets the body. On two guitars with similar body shape but one with a neck to body connection at the 14th fret and one with the neck to body connection at the 16th fret, the bridge is closer to the lower body end on the first guitar.
All individual saddles must be set close to the front of the bridge. Now take a long ruler and measure the scale length from the front of the nut (or middle of the zero-fret) and position the middle of the saddles at this point. The bridge is then located centered to the fingerboard and its front parallel to the frets and screwed on. If you don't have the long ruler measure half of the scale lenght off the 12th fret.
Setting the intonation (compensation): Put the strings on, tune and stretch them lightly to shorten the time they need to settle. Retune. Now compare the pitch of an open string to its pitch when it is depressed at the 12th fret. It should be equal but it isn't. When you depress a string its pitch becomes higher than it should be because of the slight increase of string tension when you do so. Therefore the actual vibrating length of all strings must be made longer than the scale length in order to compensate for this fact. This is adjusted when you set the intonation of a guitar. An electric guitar usually has an adjustable saddle and the necessary compensation is therefore easy to adjust by srewing the saddles further away from the nut. Don't forget to retune every time you change the string length.
Make the vibrating string length longer until both pitches are equal. That's all. You will notice that the bass strings need mor compensation than the treble strings. It might be necessary to recheck the intonation after a while when the strings have settled in completely.