As i play guitar, and get better, i once in a while decide to make a couple licks and turn it into a song. My problem is, is that i can not get the song to flow as one well. Meaning, i can not get the intro/verse/chorus to have a connection to each other. Does anyone know how i can improve on this or what i should do?

I am not sure if this helps but the music i enjoy listening to is RHCP, creed, things between those lines.
Think about why your songs don't flow. Listen to other peoples songs, and learn them. How are they connectiong their riffs/chord progressions? Though riff oriented songs are really cool, I can't really think of any songs that are riff driven through the chorus. Find some way to bridge whatever you're doing in your verse into your chorus. This may sometimes coming up with some form of pre-chorus. If you're just riffing away during the verse to a song, think about what chord changes you could play there. Use that as a pre-chorus of sorts, and then move to your chorus.

You could also try arpeggiating chords instead of just strumming them. Listen to some Rush music. Alex Lifeson arpeggiates chords all over the place, and the songs flow really well. It can often be helpful when you're trying to build a section up some without filling that section of a song with powerchords.

On the topic of chord arpeggiation, if you've got a chord progression that you've written in arpeggios, and you're having trouble with a chorus or verse, strum the chords, really think about what you're playing, and where you wanna go with it. If it's major, do you wanna switch to the relative minor, or vice versa?

Try not to think of your songs as individual parts. Try to consider what you want the overall sound to be like. Do you want it to be agressive, depressing, soft, uplifting? What is it that you're trying to express with a song? This often helps when you're stuck with a song and don't know where else to go with it.

Also, keep in mind, that when you first start writing songs, most of them suck. Don't be discouraged. Believe it or not, songwriting is a skill that you pretty much need to develop, even if you are very gifted at it. Over time, you will get better at coming up with additional parts for you songs.

Listen to some of the bands that you listed though, and really think about how they're making all of these sections tie together. This will probably give you some insight as to what you're doing wrong.
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I don't think it's about key changes or time changes like someone said. It is, in fact, a matter of linking the parts. You've already identified your problem. You should come up with bridges, breaks, or interludes so that it can flow together. If you have rhythm parts, make them flow together, because if they do, it won't really matter if the leads flow, as long as it matches the chords of the rhythm.

Also, alternative bands like creed usually use bridges to link verses and choruses, at least of what I've heard of those types of bands (don't really listen to much alternative). Look at some tabs of songs by creed that sound kind of like your song, and kind of base your song off of it. That's what I did when I first started writing, and now I'm able to keep music flowing like it's my second nature. Just try to make it the best you can, and as you get more experienced, you'll find that songwriting starts coming very easily.
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I think that what the guy meant by key changes was simply if he has two parts, but they are in seperate keys. One being in F, the other being A, or whatever. Going from a major key to it's relative minor is very common and very useful when you want a song to evoke many different emotions.
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