Stormtrooper Armor was good in its time, and did a good job of protecting the individual stormtrooper. However, even Clones have to eat as shown in some of the examples, such as scenes at Kaminos showing them eating. So how did Stormtroopers prevent having to eliminate urine and fecal waste, at the wrong time? Did they have a enhanced digestive and urinary system that allowed a very small amount of urine and feces to be expelled at a longer time than humans?
Your question is made up of two main questions:
1. How did Stormtroopers prevent having to eliminate urine and fecal waste, at the wrong time?
2. Did they have a enhanced digestive and urinary system that allowed a very small amount of urine and feces to be expelled at a longer time than humans?
2 is probably easier to answer first:
The Wookieepedia page on Clone Troopers lists some physical enhancements that were made, in addtion to the behavioural:
...the Kaminoans tampered with Fett's DNA to ensure that the clones were primarily dominated by behavioral genes that emphasized certain qualities such as loyalty, aggression, independence and discipline in order to guarantee that the army would be more docile and less independent than their template. Additionally, the Kaminoans increased their clones' lung capacity, decreased their reaction times and improved their stamina. Certain allergies and Fett's mild astigmatism were also removed from the genome.
Since there is no mention of an altered digestion system, and the fact the the progentior is a human who has been seen eating, I think we could assume that basic bodily functions still exist as we know it.
1. So, how do the avoid untimley bowel movements?
This answer suggests that Stormtroopers are slaves who are moved around alot. My speculation is that they would either 'hold it in' or 'just go when they can'. These are highly trained, physically enhanced soldiers, who have been drilled since birth to obey and serve. I imagine that they would probably see the need as expel waste as a very short task that can be completed at the most appropriate time during their mission.
Tl;dr - They're mostly normal humans, who go to the bathroom when it makes strategic sense to do so.