Hi ... I've been using zoom G 2.1 NU for a while now. it has been working well with me for effects & recording directly to my PC since its an effect pedal & audio interface at the same time, however I decided to start using separate effects for distortion, delay, wah.... Etc. now in order to connect my guitar to my PC & start recording I need a separate audio interface but I was told that if I used the Boss effect pedals along with the audio interface there will be a lot of issues in the sound.

How can I use my guitar along with the effect pedals then connect them to my PC for recording without having any sound problems?
Just use amp & FX models in your DAW and forget the pedal completely. There are tons of free amp sims & FX sims that pretty much render most Multi Fx units useless.
Derpy Derp Derp Herp Derp
Two things...

1) I changed/'fixed' your font colour; most of UG use 'UG Black' and that was just horrible to read

2) No interface is particularly aimed at having pedals in front of it - that's not the point of an audio interface. There's nothing stating you shouldn't use pedals in front of an interface's instrument input for reasons like impedance etc. - the reason it is discouraged is because most guitar pedals are, to put it simply, not very good. They often induce a lot of noise, many use cheap parts which have undesirable characteristics, and if they're used live they also often take a beating and can develop minor faults that impair the quality of the sound.

You are much better off using plug-in effects in your DAW (recording program) in 95% of the cases you would use a pedal. In fact, I would only allow a band to use a pedal in front of my Duet's pristine pre-amps if it was a) something unique, e.g. Digitech Whammy, or expression-based, e.g. wah; b) it was a high quality pedal made from quality components and had a low self-noise or c) the guitarist was a stubborn moron and refused to trust my better judgement.
Hey, look. Sigs are back.
its perfectly ok to use pedals in front of the interface. the only degradation in quality is from what DG said, if the pedals themselves are not all that fantastic. boss pedals fall into this category. they are built very well and can handle a lot, but they typically are not super high quality sound-wise.

also, some pedals just dont quite sound the same through an interface. for example, i have yet to find a fantastic fuzz pedal sim. or maybe just one that does a good job mimicing the fuzzes i have/use. but when i use those fuzz pedals in front of the interface, it almost never sounds as good.

so unless you have to use the pedal in front (like a wah), then i would see what you can do with vst effects.