This is easy to do. Either use a guitar tuner or judge it by ear.
Pluck the open string. Tune it precisely. Now hold down the string at the 12th fret and pluck it again. It should now play exactly one octave higher than before. If it sounds sharp, adjust the saddle for that string by tightening the adjuster screw. If it is flat, loosen the screw. This slightly changes the string length and lowers or increases the pitch of the note. Now start again by retuning the open string then tuning on the 12th fret. When they play exactly in tune, the intonation for that string is correct and chords (wherever they are played on the guitar neck) will ring true.
Now repeat this for each string.
You are lucky in that the Strat has individual string saddles. Cheaper guitars do not allow individual string intonations to be adjusted and a compromise is all that can be achieved.
I would suggest that you do not touch the intonation on your strat this should be done by a qualified guitar engineer. I can do this but it is not straight forward. Search the internet as there are many sites suited to this subject.