Reduce it at the back of the stove.

Some Vermont Castings stoves - the Defiant, for example - were designed and built to function properly only when connected to a minimum 8" flue. Your stove may not work well at all with a 25% reduction in flue size. I would not connect to a 6" flue without first consulting with a certified chimney sweep or knowlegable stove shop. It may be that the 6" ss liner's smooth interior surface increases draft enough to make this change practical, but do check first.

The point mainegrower brings up is quite true. The height of the chimney would influence the operation also. I think in your case, with the reduction at the rear of the stove, you have essentially redesigned the stove to operate with a 6 inch flue. In addition to the consultations mainegrower recommends, there are a few things you can do to adjust for any changes that may occur.

Most important would be to keep the liner cleaned. That may require cleaning it once a month if you use it 24/7. The cleaning will keep the inside diameter of the liner from being reduced further from soot and creosote. Adjust the damper or air input adjustments a bit more open than before and add less wood at first. In other words, you will have to change your usual habits of loading and regulating the stove until you find out what the new characteristics of the liner have created and then remember them from year to year.
There shouldn't be a tremendous difference but if by chance there is, increasing the height of the chimney may be needed. The extreme case if there is a big problem would be to replace the stove or rebuild the chimney or add an external flue system. I doubt you'll have to go there. I personally think your major areas of concern will be more frequent cleanings and damper adjustments.

Thanks for all your advice on the new flue size. I did find a brochure for vermont castings that said the stoves produced before 1990 do not operate well on anything but a 8 inch flue. Ours was purchased in 1977!! I'm going to try reducing the flue at the back of the stove instead of at the thimble to the chimney. The draft seems really strong with the 6 inch flue but we do get some smoke when we open the top loading door to replenish the wood. I really hope this works as prices have gone up so much on all the better stoves. This one was about $700 when we purchased it.

I have owned 3 Vc stoves over the past 30 yeras and currently heat with a wood furnace. The issue you bring up is important as posts have shown. As a tech rep for a former VC distributor, I advise check the manual...the 2004 Defiant model page 6 allows a 6" chimney, I quote: "NOTE: When installed with a 6" chimney connector adapter, the Defiant may not be operated with the front doors open." Last but not least, many states now require any woodstoves used in primary residences to meet EPA emissions standards. You may want to upgrade. Check out the Napoleon EPI 1900 for your heat equivelant if you use for primary heat.

Some states are offering rebates to get rid of the smoke dragons too. Check out if your state has any programs.