First, put your tub on a cleaning schedule. This helps prevent the filter and pipes from building up stinky grundge.
Make sure to check the PH Balance regularly. A good PH is 7.4 - 7.6. Also, check the recommende use of sanitizing chemicals. Your levels of these may be too low. A high PH and low chemical combination can cause an unpleasant smell.
Also, if you notice and mold around the inside of your cover or the edges of your tub you will want to scrub and disenfect those areas immediately. A solution of diluted bleach works great for this. Don't forget to check up under that flap in the creases.
One last thing does not help keep the smell away but will help the tub smell better is adding a smell good product.
Enjoy you hot tub and smell wonderful doing it!