First off, getting good at recording/mixing ain't a trivial pursuit. It takes a lot of time and is as much an art as science. It takes developing an ear which pleases you and your client (or style of music if you are doing it on your own). If you are in Medical school, I wouldn't worry about getting good at recording/mixing for a few years - after school and once you get est. Then you'll have money to indulge this passion and time, unless you get married and have kids, but that is another subject.
It sounds like you have some time-based effect on the guitar(s). The guitar should be mono, but once it goes through a stereo effect it will spread out across the field. So even if you move the mono signal, the rest of the effected signal will still be spread. Track back the signal from output to source. As above, putting a guitar through a bus or send will give you control over the mono placement, even as the reverb/echoes bounce around (think of Whole lotta Love by Zep and the guitar coming out one side and the single echo out of the other).
separation is a discertation-worthy subject. Much of it has to do w/ performance and capture and arrangement. Guitars (at least amped guitars) are compressed and band-width limited already. You usually don't have to roll off the high w/ a filter, but you can clear up a lot of energy by setting the high pass filter higher, thus limiting the low end energy. If you have several guitars, you can alter this (and maybe increase certain frequencies) so that the guitar signals separate. You can also run an eq in the guitar buss to shape the overall tone of the guitars to separate them from synths a little. Also, try the SSL buss comp in the Prochannel on the guitar buss. It can shape the guitars' dynamics so the wall of guitars allows the leading instrument to poke out - above the wall.
Synths are ususally full range and contain many if not most frequencies. As such, it helps to filter them out even harder so what is left is the important part of the signal. That keeps them revalant as well as from eating out all the other frequencies. Again, using the buss comp can keep them under control except for the loudest synth, which will poke above the rest of them. That is a hard to describe thing, except you've heard it on just about every song ever released.
Panning, of course. Typically I'll use two rhythm guitars panned pretty hard to left or right. A lead guitar goes center, along w/ the main vocal and bass. Everything else goes somewhere inbetween, so every instrument has it's own space in the soundscape.
Those are basic tools to use and watch for, esp. when you are recording and designing the sonic part of the song. Even if you have someone teach you them, there is still the refining process where you learn which tricks you like on your music, much less learning the fine tuning for other genres. It all takes time, which you say you don't have enough of. So rather than trying to make your songs sound professionally done in the genre, consider the time you do have as fun and learning the basics. Every song is a learning experience, not a finished product, and the whole experience will start clicking at some point. The idea is to not make it perfect, but better, while you learn the tool. If five more years you listen to the song, think "I should have done this or that," but find the song well done, even w/ the flaws. Sometimes I'm agast at stuff I did a few years ago, but mostly it is saying to myself, "that ain't half bad." which is the most important trick, not always listening w/ a critical ear but enjoying the end product. A lot of the stuff you fuss over at the time dissappears when you listen later. Because you can always improve a mix, but at some point it is time to finish it.
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