The best thing you can do is not wear your boots two days in a row. I know that may mean another pair of boots. But the reason for this is to allow all the moisture that builds up in your footwear to evaporate. Otherwise your boots will be damp all the time and this will allow the insides to start breaking down from the perspiration. This is really important in footwear today that is made with cushion insoles instead of leather insoles. The foam cushion will start to break down pretty quick from moisture if it is not allowed to evaporate.
If your not is a position to own two pair of your favorite boots, then try to use a boot dryer, like Peets, if you have access to electricity when hunting. If not, then another way is to stuff your boots with newspaper and this will help absorb the moisture.
I would not fill your boots with soapy water and then let them soak ect. This will just enhance the breakdown of the insides of your boots. Even in the days of leather insole, or traditional insoles, you only soaked your boots if your breaking them in. The leather insole would then form itself to your foot thru out the day as it dried out. As I mentioned above with today's cushion and lining on the inside you do not want to do this as a break-in or as a cleaning method.
There are products that you can spray inside your boots to help with odor. Or you can use talcum powder.