I'll point you toward this book for your theory needs, because it is cheap, practical, and relatively easy to understand:
Hal Leonard Pocket Music Theory: A Comprehensive and Convenient Source for All Musicians: Carl Schroeder, Keith Wyatt: 0073999309683: Amazon.com: Books
Next, this is a guitar chart that I made for the benefit of this thread:
ChordsInAKey
Without getting too deep into the theory stuff, a given major or minor key contains a number of chords of different qualities (major, minor, and diminished). If you play the correct chords in a sequence built on their corresponding note in the major or minor scale, you make a chord progression. This chart is a quick and dirty guide to knowing which chords are in the scale. I should begin by saying that the chart is meant to be freely transposable, meaning that you can move it up and down the fretboard and so long as the relative distance between the notes is consistent, everything will be just peachy.
There are two pieces of information here that you have to match: the diagram of the scales (the ones with the square fret markers) and the diagram of the chord shapes (the ones with the circle fret markers). There are some numbers inside of the fret markers, but it is not necessary that you understand what they mean if you are just getting started. What is important is that you match up the "1" on the chords to their respective place on the scale. So if I wanted to play the chord built on 2 in the major key, I would need to play the minor chord shape on the spot that corresponds to 2 on my fretboard.
Once you've got a handle on matching the correct chord shape to the scale, you can try out some common progressions. Play each line and then repeat it to your heart's content before moving on to the next:
Common major key progressions
1 4 5
1 5 4
1 6 4 5
1 5 6 4
1 4 2 5
3 6 2 5 1
Common minor key progressions
1 4 5
1 ♭6 4 5
1 5 ♭6 4
1 ♭3 ♭6 2 5
1 ♭7 ♭6 5
1 ♭7 4
Songs are organized into sections, which are organized into phrases, which are organized into measures. When you are counting "1 2 3 4, 1 2 3 4, 1 2 3 4..." you are counting the beats in a measure. "1" is the start of a new measure. Typically, a chord will last for the entirety of a measure. Here is an example of a chord progression that has one chord per measure:
1|4|5|1|
Each | marks the end of a measure. This means that you strum the 1 chord for four beats, then the 4 chord for four beats, then the 5 chord for four beats, and then the 1 chord again for four beats. Here is the same thing, but with the same chord over two measures:
1|1|4|4|5|5|1|1|
This time, each chord is getting eight beats. Referring to time in music by beats gets tedious after a while, so this is simply one chord every two measures.
This is an example of a common phrase structure called a twelve-bar blues. It consists of three phrases of four measures each:
1|4|1|1|
4|4|1|1|
5|4|1|1|
Phrases are most often eight, twelve, or sixteen measures in length. Here is an eight-measure phrase:
1|6|4|5|
6|4|5|1|
Here is a sixteen measure phrase:
1|6|4|5|
6|4|5|6|
1|6|4|5|
6|4|5|1|
Sixteen measure phrases can often be broken down into two eight measure phrases, hence the line I put between the first and second half of the phrase.
Once you have learned how phrases are structured, you can make them into sections. A section consists of at least one phrase, but you can repeat that phrase as many times as seems fit. You can then combine two or more sections in sequence to get something that feels a little more fleshed out. Sections are called by letter names, so we would say that the first section is the "A" section, the second section is the "B" section, the third section is the "C" section, and so on. Here is an example of a potential song:
A section:
1|4|1|1|
4|4|1|1|
5|4|1|5|
(repeat)
1|4|1|1|
4|4|1|1|
5|4|1|5|
B section:
1|1|1|1|
4|4|1|1|
5|5|4|4|
1|1|1|5|
A section:
1|4|1|1|
4|4|1|1|
5|4|1|5|
(repeat)
1|4|1|1|
4|4|1|1|
5|4|1|5|
B section:
1|1|1|1|
4|4|1|1|
5|5|4|4|
1|1|1|5|
C section:
6|6|6|6|
4|4|2|2|
5|4|1|5|
(repeat)
6|6|6|6|
4|4|2|2|
5|4|1|5|
B section:
1|1|1|1|
4|4|1|1|
5|5|4|4|
1|1|1|5|1| (Added on an extra chord to complete the song.)
Notice that when I bring back a section that I have previously played, it retains its letter name label. This allows us to analyze the music effectively. The overall form of this song is ABABCB, meaning that there is an A section, then a B section, then A again, B again, C, and finally B at the end. A very common form. Feel free to steal that; my potential song is a very generic model that you can imitate or modify at your own whim.
Anyway, I hope this helps you to write your first song. Let us know how it goes.