This is what I do every time without fail for composing and arranging (which I do at the same time):

1) Create a collection of riffs that flow well from one to the other
2) Set the correct bpm (tempo)
3) Record the most basic core riffs to a click
4) Work out a basic midi beat that suits the riffs
5) Re-record all riffs to the new beat as it has an impact on inflections and can alter things slightly
5) Then I set about working on the first section without any thought for what is to come after it... I find that by doing this I can create more easily as it is much easier to work into a blank canvas than a predetermined structure
6) Once the basic rhythm riff is in place, I record it again and pan to each side
7) Then record the same riff again but on one string (instead of power chords) and use plenty of vibrato and harmonic pinches
8) Record a harmony to the riff up higher on the fretboard, perhaps using some notes that would create a chord. Multi track recording for rhythms makes things sound a lot more impressive and full.
9) I record the bass-line last because I am a guitarist and I don't want the bass to sound just like the guitar. So rather than be lead by the riffs, I look at it after all guitars are done and play along to the drum beat with the riffs in mind. Another benefit of doing it after the guitar parts is that you may have new ideas for counterparts or harmonies that could sound great on the bass but not so good on the guitar.
10) Now get the collection of riffs (each recorded onto a separate track on Cubase) and arrange them (using copy and paste with the 'snap' to 'beat' or 'bar' function)
11) You can experiment to see what sound is best introduced where (eg, beats first, then bass, then guitars or guitars, then everything, or even everything at the same time etc). The more experimentation you do, the better ideas you will come up with.
12) Export to MP3, burn to cd and drive/sit/walk around for a few days listening to it non-stop. Doing this gives you the opportunity to critique what you've done without going too far into the song. But more importantly it allows you to imagine what would sound good next and what melodies/harmonies.lead parts would sound good over what you've done so far. Just imagine the parts in your head, hum it aloud or sing it, if you can write music, jot it down, or if you are out and have an amazing idea, call your cell phone and hum the idea onto your voice-mail. It feels a little weird at first but it saves you from losing ideas. Some players like Marty Friedman carry a little tape recorder with them everywhere and sing ideas into it.
13) Now the real fun start;-) Just work out the ideas (leads, melodies etc) you've come up with in the same fashion as above (changing and re-recording previous parts to match the entire composition as you go along).
14) The last thing I do is the final drum track. It's tedious, boring and very difficult but you can use the original beat as a guide. Try making a recording of everything with the drum track muted out. Again, put it in your car or walkman or whatever, don't listen to any other music for a few days and just imagine what would sound good over it. Try tapping the beat out a few times, it gives you a better idea of which drums to use where and helps to create better grooves.
15) That's it... if you can, export as 44100 x 24 bit and make sure that all tracks you record are wav files in the above format - no MP3 files!!!
16) Last bit of advice, use the volume control and pan function as often as you can, it makes things easier to hear in the mix. Just experiment until you get something you like.
This is the way I do things, other people do it different ways. Hope. this helps
As you can see, I am having a quiet day at work!!

NOTE: I forgot to mention, when you record any part make sure that you give yourself at least 1 bar of an intro after the click. Recording straight after the click will result in a wav file that sounds unnatural (starts too abruptly). You can always edit the file later to remove any unnecessary silences. This also apples to ending wavs, leave a few seconds of silence after each riff and edit later.