Im confused, with all this theory stuff, I dont know where to start, fist I learned the notes on the fretboard (not memerized, but i can find certain notes), but I dont know how I should learn scales or in what position, so could somebody please tell me what to do?

Now im an high intermediate player, and I know what im doing playing, I can play very well if I may say so for myself so I really need to kick it in gear and learn how to improvise and do this and that, but im very confused
Ummm first off. If you are just learning the notes on the fretboard you are by no means a "high intermediate player". Even if you can play every single little AC/DC, or Van Halen (or whatever else 13 year old boys are obsessed with now) song note-for-note you are no means a intermediate guitar player. You're simply a regurgitator. Go on Amazon and find a theory book. Mel Bay makes OK stuff. Go find it now.
a little lie says you'd like nothing better.....
Try making pedal tones with the root notes in scales. That's a good springboard for improvising solos and things.