I have long hair right now, and I'd like to keep it that way when I get a system, would there be a problem making it not look like a wig if my hair is about 6 inches long and wavy?
There is no reason a long hair system should look 'wig like' at all. As long as you have a good quality system with good quality hair, the right density and a good cut in, you'll be fine. Hair systems these days look totally realistic if done right.
Another question I have is how hard would it be to maintain having dyed hair, I know I'd have to order a system with the color already in it but I feel like my bio hair underneath would grow out it's natural color and would need dying every so often because the roots would come through eventually and people would be able to tell it's a wig if I'm not careful. Can this be realistically achieved?
There is no problem at all about dyed hair. If you dye your real hair, you can send a sample of it to the company who makes your custom system (or ask them for a colour ring to match to the colour if you prefer) and they will match the colour on the system to the colour of your dyed hair as closely as possible.
Hair systems can also be dyed, but you have to know what you're doing in order to do that successfully (or get an experienced stylist who is good with hair systems to do it for you). But in theory, you could potentially dye a system the same colour as you dye your real hair to get an exact match. This wouldn't be my first recommendation, but it can be done.
I don't see it being a problem about your bio hair underneath the system growing out. When you have a long hair partial system, the partial is going to have enough length to cover where your bio hair starts at the back and sides, so nobody will be able to see the roots of your bio hair anyway. Also, you can easily touch up the roots/redye your bio hair every so often if/when you notice the roots growing through. And even if your bio hair is a slightly different colour to the hair system, that won't necessarily look unnatural - people with long hair do that all the time, i.e. having different layers of hair in different colours for effect. As long as the hair itself looks real, it'll look fine.
Oh and avoid using the word 'wig'. A 'Hair System' is not a wig, but an integrated, undetectable semi-permanent hair replacement solution, as clarified in this blog post:
http://www.hairhub.com/blog/exactly-hair-replacement-system-wig/
I just think that once you dive in and go for it, you'll easily find solutions to these minor little issues and they won't be problems at all really.