Even with a good reflux still with a long column you'll get some flavours and smells carrying over unless you are really meticulous with temps and take product really, really slowly. None of them will make you sick (as long as your not being too greedy and your making the cuts at the right places-read easy to do) but your product will still be a little smelly. You could do a double distillation (ie. run it through again) or let it sit on carbon. In my opinion it's far better to let the spirit sit on the carbon than filter it, it just basically comes down to how carbon works, it's about contact time. The longer the spirit is in contact with the carbon the more time it has to soak up smells and off flavours. Two weeks usually does it.
I add a good tablespoon per litre straight into the bottle, however firstly I will boil the carbon in water on the stove then pour off the excess water and then add it. This just drives off any off flavours that may already be in the carbon and rehydrates it so it's ready to get to work.
Read www.homedistiller.org for all the info you could want in all aspects of distillation.
Cheers, JD