Well, whoa, here..... are you putting those rocks in as "new" rocks? If so, yes, you can boil and sterilize them. This is particularly important if the rocks have been used in a tank before. That way you can be sure you are not transporting nasties into your tank.
If the rocks are already in your tank, no, you do not want to boil them. They can, and do carry a bit of beneficial bacteria - and, depending on your tank/filter situation - this bit may be very important to your tank's cycle.
The rocks, themselves, should not cause the water to take on a color -all that should happen is, if there is lots of "rock dust" that is on them, the dust will make your tank cloudy until the filter has a chance to filter it all out.
As for the "root", many real roots and wood pieces have a natural substance in them that is called tanin. It will leech out of the root and wood as it soaks in the tank, and colors the water reddish or orangish. It is a harmless substance - if you have been to water swamps and such in the south, you will see water with heavy tanin coloration - it is natural and harmless. But, it is very unsightly in a tank in your house. You can soak this root in water, changing the water daily or weekly for several months to remove the majority of the tanin, or you can boil it, with about .1% salt in the water bath, for about 20 minutes and remove the majority of the tanin.
Remember - a real piece of wood or root in your tank becomes a source of bio-matter/waste that can lower your tank's pH over time. Make sure you check your kH carefully to make sure your buffer can hold its own against that waste.