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clean DI and effected amp signals

I record my bass through DI. I use pedals and ampsims at home. Usually I end with CLEAN DI before effects and DI with effects (fuzz, chorus) which then I'll send to ampsim software. But when I blend these signals together there's a mess. I know about phase issues and I can get good tones. But is this OK to have clean DI and blend it with effected AMP? Or should I mix effected DI and effected AMP? What's the practice?
 
You said you know about phase issues. That's really all there is to it. You have two sources with a varying phase relationship. Either you like the sound of them together or you don't. If you want a clean signal blended in with an affected one then do that, but realize you'll have phase discrepancies to deal with in post. If you don't need a clean signal blended in and want to use two signals, then by all means use two affected DI signal paths. You'll still have phase discrepancies as phase is not only time dependent, but also frequency dependent. If you take two clean signals and apply a simple EQ you'll still have to deal with phase problems to some degree. My favorite solution is to get what I need from a single source and not have any phase problems within the bounds of a single instrument.
 
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