This is a good question.
To get a better understanding of the Be Bop scales and some of the rules/tricks to using them get a copy of David Bakers "How to Play Be Bop" book series. David does a great job of explaining how to use the Be Bop scales (what they are when to use them etc..) and provides a ton of examples of phrases over typical chord changes.

The great thing once you get through his book(s) is that you can quickly analyze what is going on and come up with some really interesting and original phrases.

All the best!

Hey Soren,
I would agree with playing with your heart.
A good practice is to play what you hear in your head. Play a song and sing a phrase then replicate it on your instrument. Keep on doing this one or two bars at a time or however long the phrase you is that you think/sing.

You mentioned playing the 1 3 5 7 of the chord which is cool but start practicing approach notes to these appregios. Create studies where you always approach the 1 from a half tone above or below. Then do the same for the 3 5 and 7 of the chord. When doing this "run" the pattern diatonically in a key. For example, start on the one chord using the approach note to the 1st note of the appregio then approach the 1st note of the next chord etc...

After that mix it up by approaching the notes either 1 half step above or below and then also approach the notes by a whole tone above or below. Then approach the chord tone a half step above then a half step below then play the chord tone. Then do two half tones below then two half tones above. Then you can do two half tones above and a single half tone below then the chord tone.

By doing studies like this you start getting these sounds under your fingers and into your head where they become natural to play. If some of these combinations don't sound good just don't play them and concentrate on the ones that work for you.

And lastly, where I think things start to really open up is doing "hybrid" interval studies where you pick to intervals and alternate between them when running through scales.

For example: You pick intervals of 3rds and 6ths.
Using the C major scale you would first play the 1 and then the 3rd (C to E which is a third apart) then you would play the next scale tone which is the 2nd D and the 6th of D which is F. Then move to the 3rd of the scale and play the 3rd of that note and then play the 4th of the scale and play the 6th of that and keep on going until you reach the octave of the root of the scale ( in this case C) and then start playing it descending using the same pattern. The pattern in a nutshell goes like this:
1,3,2,4,3,5,4,6,5,7,6,8,7,9,1 then backwards descending start like 9,7,1,4 ...

These studies should keep you off the streets for a long long time! By doing this you will find some very interesting patterns and sounds that you like. After a while you will just do parts of these studies automatically.

Transcribing is also very important. Find songs and phrases that you really like and would like to add to your vocabulary. You will learn tons from transcribing.

So, I guess that just about covers it!

Remember though the most important thing is to play what you feel and hear. These studies are meant to help you expand your vocabulary and push your dexterity to do things that you never have done.

All the best!

Gerry