Regarding the 9th, you will mostly use it in 2 situations: to enhance a major chord and to replace/alter a 7th chord
Enhance a major chord
When you add the 9th to a major chord, it becomes an add9 chord. This will make your major chord sound more "pretty" and "lush". So, basically any time u got a major chord, u can add the 9th. Example:
Cadd9 = C-E-G-D, E-G-C-D, G-C-D-E
Now, u pointed out that the 9th note is the same as the 2nd. Since that is true, u can also play this chord with the 9th in the position of the 2 and still have the add9 chord:
C-D-E-G, D-E-G-C
Replace/Alter a 7th chord
Any time you want to play a 7th chord, u can add the 9th and make a 9th chord. Not only can u add the regular 9th, u can also alter the 9th. So, u can have a b9, regular 9, or a #9. Each option gives you a different sound. Examples:
C9 = C-E-G-Bb-D or C-E-Bb-D
C7 #9 = C-E-G-Bb-D# or C-E-Bb-D#
C7 b9 = C-E-G-Bb-Db or C-E-Bb-Db
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CM9 = C-E-G-B-D or C-E-B-D
CM7 #9 = C-E-G-B-D# or C-E-B-D#
CM7 b9 = C-E-G-B-Db or C-E-B-Db
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Cm9 = C-Eb-G-Bb-D or C-E-Bb-D
Cm7 #9 = C-Eb-G-Bb-D# or C-E-Bb-D#
Cm7 b9 = C-Eb-G-Bb-Db or C-E-Bb-Db
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CmM9 = C-Eb-G-B-D or C-Eb-B-D
CmM7 #9 = C-Eb-G-B-D# or C-Eb-B-D#
CmM7 b9 = C-Eb-G-B-Db or C-Eb-B-Db
Notice here that each of these chords has to contain the 3rd and 7th. The 5th can be left out if you want. Also notice the naming of the chord when u add in an altered 9th. It is a 7th chord with the added 9th.
O.K., now that we got the theory out the way (LOL), let's talk about specific places where you would want to use these chords. Take the add9:
1-4-5 progression in C
C / G-C-E
F / F-A-C
G / G-B-D
now, let's play add9 chords:
C / G-C-D-E
F / F-G-A-C
G / G-A-B-D
Hear the difference between the 2? Now, u may not want to play an add9 chord for every major chord, but you can if you want to. Just go with whatever you are feeling at the time.
Now, let's deal with a M9. I said ealier, u can use this chord when you play 7th chord. In this case, I like to play major 7th chords on 1 and 4. So, let's start with a 1-4 progression:
1-4 progression in C
C / G-C-E
F / A-C-E
Now, let's play those chords as M7 chords:
C / G-B-E
F / A-C-E
Now, let's play those chords as M9 chords:
C / G-B-D-E
F / A-C-E-G
Hear the difference between all 3? Just pick what works best for you. You don't have to play M7 or M9 chords for both, but u can if you want. Heck, u can even mix up using an add9 and a M9 chord. Let's do it:
1-4-5 progressions in C
C / G-C-D-E (Cadd9)
F / A-C-E-G (Fadd9)
G / G-B-D (G)
C / G-B-E (CM7)
F / A-C-F (F)
G / A-B-D-G (Gadd9)
C / G-B-D-E (CM7)
F / F-A-C (F)
G / G-A-B-D (Gadd9)
C / D-E-G-C (Cadd9)
F / A-C-E-G (FM7)
G / D-G-A-B (Gadd9)
The possibilities are endless. Plus, you can use all 4 in the same song, that way everytime you play it will sound a little different than before. This is how the pros can play a simple tune and never play it the same way twice, cuz u got options.
One more then I will let you work with it. Let's deal with the dom.9 chord. The dom.9 chord will work anytime u have to play a dom.7 chord. I play dom.7 chords on 1, 2, 3, 5, and 6. Dom.7 chords resolve to 4 of the chord, so let's see some examples:
1(dom.7)-4 progression in C
C / C-E-G-Bb or C / E-G-Bb or C / E-Bb (C7)
F / C-F-A (F)
Let's change that dom.7 chord to a dom.9 chord and see how it sounds:
C / C-E-G-Bb-D or C / E-G-Bb-D or C / E-Bb-D (C9)
F / F-A-C (F)
You hear the difference between the 2? Cool, now let's play these chords using an altered 9th to see how it sounds:
C / C-E-G-Bb-D# or C / E-G-Bb-D# or C / E-Bb-D# (C7 #9)
F / C-F-A (F)
C / C-E-G-Bb-Db or C / E-G-Bb-Db or C / E-Bb-Db (C7 b9)
F / C-F-A (F)
Hear the difference? Each one gives you a slightly different sound and mood. You should experiment to see which ones u like and try to make your choices fit the mood u want to convey.
The same process can be applied to the other times I use dom.7 chords which are:
2(dom.7)-5 progression
3(dom.7)-6 progression
5(dom.7)-1 progression
6(dom.7)-2 progression
Now, keep in mind that some of those progression up there end with minor chords. Those are 3(dom.7)-6, 6(dom.7)-2, and 2(dom.7)-5. So, just experiment to find what sounds you like, and if u need more help just ask.