It sounds like the reason it stinks is that it is wet. Three things can happen to organic material. Organic material can be bedding, food, or poop. If it is too dry for microbes to live and reproduce it does not decompose. It just sits there. It doesn't small and can stay forever. If it is damp enough for the microbes to get enough moisture to live and reproduce but not too wet for them to get fresh air, aerobic microbes break it down. You don't get a bad smell, more of a healthy earthy smell. If it is too wet for those aerobic (oxygen breathing) microbes to get oxygen, anaerobic microbes take over. Their waste products create a strong smell and can be pretty slimy. A wet brooder, coop, or run can also harbor diseases.
Where is the wet coming from? It could be from the environment somehow, maybe rain getting in there. Or it gets wet and just doesn't dry out. Your waterer could be leaking, unless the type of waterer you are using is perfectly level they can leak. A very common cause is that the poop builds up so thick that it doesn't dry out. It often takes two or three days for those anaerobic microbes to build up to a smelly level.
Chickens poop wherever they are, during the day and at night. Since they are not moving around at night the area under the roosts often see a huge build-up of poop which can stay wet. Even of we have a huge amount of room many of us use droppings boards to manage that build-up. If space is really small they may not roam around enough to spread the poop out so daytime poop can build up too.
The way to eliminate the smell is to get rid of the wet and keep it dry. So where is the wet coming from?
If you follow the link in my signature below you can get some of my thoughts on space requirements. I've noticed that the tighter I pack them the more behavioral problems I have, the harder I have to work, and the less flexibility I have to handle issues that come up. It sounds like you may be experiencing the last two. You don't have any flexibility in how you manage that other than to work harder managing the poop if poop build-up is your real problem. If the waterer is leaking fixing that may help you but I really think the poop build-up is your core problem.
Each flock is different and we manage them differently. Even if you follow the general guidelines as far as square feet per chicken you can still run into problems. Or you may find that it is more space than you absolutely have to have, especially as far as behavioral problems go. The work harder and flexibility parts still hold true, whether they are huge Jersey Giants or tiny Seramas.
My general advice is to provide as much room as you reasonably can. I don't know what you have to work with. And go by what you see as opposed to what someone over the internet like me tells you that you will see or have to do. I think with that smell and how hard it is to clean what you have it's already telling you that you need more room.
Hello and welcome to BYC. You found an Amazing Poultry Community to be a part of with many knowledgeable members who are willing to help you along your journey with any questions you may have. Enjoy 
