I use recording software (Cubase).
I set the song length to about 3 1/2 minutes, make an intro of 4 bars, a first verse of 4 bars, a chorus. Then a second verse of 4 bars and back into a couple of repeats of the chorus. Then a bridge and finally repeat the chorus until the end of the song.
You can buy drum loop CD's in REX format that are already set up with intro's, verses and chorus etc. So you just use those set up the basics of the drum tracks.
Then you record a dozen or so tracks of just jamming on the guitar, keeping in mind where the verses and chorus's should be.

Once you finish, you pick what sounds best and then start adding the rest of the instruments.
If you change your mind about the order of the different parts of the song, it's just simple cutting and pasting to move everything around.

As you spend a few weeks on a song like this, all kinds of ideas start coming to you and you just keep what sounds good and mute out the rest.
You'll also start coming up with melody lines and lyrics.
Last step is to add vocals and harmonies. Mix it all down. Master it, burn a bunch of CD's with about 12 of your songs, do the cover art etc.
Buy a bar code and send the album to CDBaby. Authorize digital sales.
Upload demo versions to usenet and other online resources. Send copies to online radio stations.
Then just wait for the money to start coming in.

Don't expect much though. I sell tons of songs through iTunes etc., and at about .0003 cents per song, I only make maybe $20 a month from digital sales. The real money is in music for TV/Film and loop CD's.

Anyways..I digress....
Most popular songs are in the normal structure that's been around for years.
intro, verse, chorus, verse, chorus, bridge, chorus, fade to end
... or other slightly different variations.
The intro has to be short so it gets to the vocals fast, the verse has to happen quickly so you can get to the catchy hook in your chorus.
Hence the reason why most popular music these days sucks the big one.
Everybody follows the same formula because that's what you have to do to get played on the radio.

The indie and truly original stuff gets lost in the shuffle.