This is what I learned so far,

1. the parts of the guitar

2. the major and minor chords

3 the guitar chord chart

4. the notes on the guitar

I can play a few songs note by note, my question is, how do you add bass to do those notes so I can play it smoothly?

Another question about guitar tunings, a standard tuning is E A D G B E while drop D is D A D G B E, my question is,
is there another guitar chord chart for that tuning or the guitar chord chart is the same?

I don't have any background on music theory, I've just bought a guitar really.

In response to your drop-D question: excluding the 6th string, everything is the same as before so you can play regular chords that don't include the 6th string, or simply don't include the 6th string in chords that involve all 6 strings.  However, you do have a shiftable power chord that can be played using one finger barred across the 6th, 5th and 4th(optional) strings.  Drop-D doesn't necessarily change the configuration entirely but does open up other possibilities such as one finger  power chords, allowing the other fingers to add additional notes/riffs on top.

Regarding the bass-notes question: Are you referring to playing bass-notes and melody notes simultaneously?  If yo could let me know a bit more about this query with some song examples I'll try and answer as best as I can.