I *think* I know what's confusing you.
Just because a source is "digital" doesn't mean that the signal out of that source is digital. For instance, if you run RCA jacks out of your digital CD player into your amplifier, that signal is ANALOG.
The process of converting a digital signal into an analog signal is done using a special device called a D/A (digital/analog) converter. The process of converting an analog signal into a digital one is done by a, you guessed it, A/D converter.
The soundcard in your computer is a glorified A/D/A converter. It takes analog signals and converts them to digital. It also takes digital signals and converts them to analog.
You cannot take a digital signal and run it through an analog effects unit....well, maybe you could but it would sound like a british new wave record. The signal must be converted from digital to analog.
A/D/A conversion is probably the #1 killer of sound in the digital realm. People spend thousands of dollars on soundcards or standalone converters to maintain as much purity as possible. A general rule of thumb is to keep analog and digital seperate as much as possible...the fewer conversions the better.
BTW, digital signals are not sent over standard instrument cable as you were describing. There are several technologies used to move digital signals. The most common is probably S/PDIFF...you'll know it if you have it. You're not going to mix up your digital and analog sources. If it looks analog, then it IS analog and the signal that you assumed to be digital was in fact converted to analog somewhere. That is, RCA, 1/4" phono/TRS, and 1/8" phono/TRS are all analog connectors. If you take a signal out of a digital device with one of these, then that digital device has internal D/A conversion...and it's in all likelyhood very poor.
Slackmaster 2000