So I finally got all of my equipment set up, Im recording fine, ect. But Im having alot of trouble editing the stuff I get on the computer, Im using Cubase LE 4 but my questions are pretty general.

Honestly I would appreciate it if someone could point me to some guides or articles about this stuff.

1. When you record multiple tracks how do you transition them together, especially if the riffs connect to each other, without it being noticeable and smooth (i.e. two rhythm parts)

2. How can I get all my tracks to be more audible? My whole mix seems to run together.

3. What do you normal do when mixing to make it sound better other than eqing?

Any other tips are welcome.
You can EQ, you can stereo reverb, delay or flange. These will give you better ambiance, but there's no substitute for practice. Digital is so much easier than the discipline that magnetic tape needed.
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Before you even try EQ, are you panning anything? Provided that your recorded tracks have been captured with any kind of decent sound, taking full advantage of the stereo field is one of the most powerful tools you can employ when mixing, to seperate sounds.

After you've figured out how to pan things around to free up some room in the stereo space, then you can start using EQ to free up some energy in the frequency spectrum, but once again, before you try really EQ'ing, try high-passing instruments that don't utilize frequencies below 100-200hz for example, and low-passing instruments that don't utilize frequencies above a certain point.

Those two things will free up a lot of space and sound and open up your mixes a lot before you even start playing with EQ curves or throwing on a ton of FX.

Speaking of FX, wet FX like reverb, delay, chorus, flanger, phaser, can make things sound faint and distant in a mix, compared to dry tracks. Try holding off on those as well until you've worked on panning and low-passing/hi-passing.

Hopefully that's not too much info all at once.