I have heard before it is good to record clean audio in a separate track and apply effects later. I am very new to this and any advice would be appreciated.
If I understand your premise—you want to record bass lines in the highest quality now so that you can just manipulate them later and not have to rerecord them—I'd reconsider that. It is great to record bass lines whenever you have an idea but not a full song yet because it could easily turn into a song later or be useful in some way.
But getting a great bass sound in the final mix isn't really a matter of how clean you record it initially. In fact you usually want to get as close as you can to your ideal bass tone before FX (plugins, etc) are applied. And you want to do that in the context of the song. So if a particular song requires a specific tone, start with your technique, your instrument, your pedals, and your amp. Tweak the EQ on your amp before you start thinking about EQ plugins, etc.
Of course, if you don't have a song yet, you probably don't know exactly what tone you want yet. And there's the rub. Even if you did, it's hard to get the feel and technique correct when not in context of the song and hearing how different instruments interact. In a band this requires playing the song together for a bit to get a feel for it. When recording solo, this usually means recording and re-recording until it all works together rhythmically and the mix gels at least a bit soncially. Then … it might be a good time to break out the FX for finishing touches.
In other words, if the dry bass (no added FX) doesn't work as far as rhythmic feel and isn't at least most of the way to your desired tone, piling on FX probably isn't going to help much. Just re-record the part again later within context of the song.
That said here a few tips:
- (before every take) Are you in tune?
- Consider every aspect of your signal chain starting first with you then working outward. Could your finger/pick technique get you closer to the desired sound? Flat vs round string winding? String gauge? Neck/bridge pickup? Tone knob setting? Different bass or type of pickups altogether (P vs J, etc)? Pedal settings? No pedals? Different amp or cab? Amp settings? Mic placement? Mic? Direct instead of mic?, etc… The more of this you get right before FX the better. For instance there's no plugin that's going to make a pick sound like fingers or vice-versa.
- Watch your gain staging. Two particular pain points for beginners are with preamps (if using mics) and digital converters. Like all amps, preamps have a certain amount of headroom and can introduce noise when cranked. So if the sound source is so quiet that you need to crank the pres way up, instead try turning your amp up a bit so you can turn the pres down. Then watch that overall level as it is hitting your converters/interface. You don't want a signal so soft that you'll need to digitally boost it a lot later, but you also definitely don't want to clip.
- If using a mic, make sure it matches what you're looking to achieve. If you want to capture the lowest frequencies then make sure the mic can even handle those frequencies (ex. D112, D6, etc). But not all bass parts have thumping sub-bass and a mic that accentuates the bass' midrange (ex. RE20, MD421) might be better depending on context.
- If you can record by a dry track as well via some kind of DI output, go for it. Yes, put it on a separate track. You might not need it and don't use it in the mix just because you have it. It's okay to mute what you don't actually need. But it doesn't hurt to have it or to try out DI vs mic or a blend of the two. That said, watch out for phase issues when blending multiple mics or mic and DI. You might have to nudge one or the other so they line up.
- If you don't have mics or a budget for some, recording only direct can be option too. But my caveat about context within the song still applies. If you have some kind of preamp or amp-in-a-pedal type DI that can work great too. Just try to dial in a real tone that you want for the song because that will effect how you play. For instance you may end up adjusting your technique, even if you don't realize it, when playing with high-gain tone rather than with a clean one. The same goes for software amps. Dial in the sound and use it while tracking so that even though the actual recorded audio will be the unaffected DI sound, it will be played in a way that matches your eventual tone with the simulated amp.