Try first writting song in just one key. So if it's A minor, play your melody in the A minor scale and use the chords of the A minor key. Alittle study in music theory will help you alot here. When it comes to making two ideas come together smoothly. The key is to keep one aspect of the first idea and use it in the second idea. Like a beginning rhythm. If the first idea starts with a rhythm like "da da dada da", repeat the rhythm in the second idea. Take a listen to some riffs in rock and metal music. A riff is usually repeated four times, the first three might be the same, while the fourth starts the same, but the ending is different from the first three. It might not be exactly as I described everytime, but there is always something similar going on.

Also not every part has to be smooth into the next, you don't always want that. A dramatic change can really spark up the intensity of a song. Just don't over do it. ;)

Also a good first step for songwritting is to take songs that you like. Then write a song that is very similar, but using your own chords and scales. This is a great way to learn the inner workings of songs. Don't worry about copywrite laws, unless you write up something, sell it, get a deal, and blah blah. Use this as practice.

I do suggest reading up on some music theory, you'll find the answers there. It won't tell you how to write the perfect song but it will put alot of things into perspective. And keep practicing...