Hey & welcome!

Originally Posted by: shan333I am learning music theory thru the guitar tricks lessons ...

I suggest starting with GF 2 which provides the absolutely basic intro to music theory via:

1. Intervals
2. Scales (major & minor diatonic)
3. Chords (major & minor triads)

In GF 2 you can learn how intervals are used to build scales, chords & ultimately how scales & chords are related to each other.

http://www.guitartricks.com/course.php?input=2

After that you can continue with one of the style courses which deal with the theory & practice of rock, blues or country.

For more detailed info & concepts, just ask! For example:

Tutorials on Improvisation
http://www.guitartricks.com/tutorial.php?input=876
http://www.guitartricks.com/tutorial.php?input=483
http://www.guitartricks.com/tutorial.php?input=491

Intro To Music Theory
http://www.guitartricks.com/tutorial.php?input=495

Intro To Circle Of Fifths
http://www.guitartricks.com/tutorial.php?input=835

Intro To Modes
http://www.guitartricks.com/tutorial.php?input=370

Practicing Modes
http://www.guitartricks.com/tutorial.php?input=770

Chord Triads & Inversions
http://www.guitartricks.com/tutorial.php?input=148

Practicing Triads & Inversions
http://www.guitartricks.com/tutorial.php?input=730
http://www.guitartricks.com/tutorial.php?input=731
http://www.guitartricks.com/tutorial.php?input=733
http://www.guitartricks.com/tutorial.php?input=734

All this stuff does work together. It is ultimately all integrated. But only after much thinking & practicing. Exactly as you point out. :)

Let us know how it goes or if you have more questions. Best of success & have fun!