Our Gemara on Amud Aleph refers to the classic Talmudic principle of עשה דוחה לא תעשה, that is, a positive command in the Torah is taken to override a negative prohibition. The Shalah (Aseres Hadibros, Yoma, Derech Chaim 62) wonders why the Torah describes various punishments for transgressing prohibitions (death, Kares, lashes) but is silent regarding the punishment for refusing to obey a positive mitzvah. This counter intuitive as the same or even greater obligation is a upon us to serve and obey the directives of the Heavenly King. Furthermore, he wonders, if we were to conclude that the absence of explicitly stating any punishments for non-performance of a positive commandment indicates a lesser severity than a prohibition, how it it possible that a positive commandment overrides a prohibition?
Shalah explains that each mitzvas aseh (positive command) is vital, and if left unfulfilled, there is an incalculable and infinite lost opportunity. All the purgatory and suffering in the next world will not equal the bliss of even one mitzvah. This is why the punishment for neglecting a mitzvah cannot be described, as unlike a negative prohibition, the loss is infinite.
Shalah then goes on to develop a fascinating idea. He likens each mitzvah to various natural forms of sustenance that are all key, but different. For example, you can prepare for a journey by bringing adequate supplies of food and water. All the food will not substitute your need for water, nor will all the water meet your needs for caloric intake. And, even if you have food and water, without air, you will suffocate. So too, each mitzvah fills a vital need and neglecting any single one can lead to catastrophic spiritual loss of vitality. Furthermore, this is why we find that certain tzaddikim were known for zeal in a particular mitzvah. This is because they were attuned enough to know that their gilgul (current iteration of a series of reincarnations) had fulfilled certain mitzvos to completion, but needed specific repair (tikkunim) in other areas. This is only in regard to people who are holy enough to sense their spiritual dashboard, but the rest of us must chase every mitzvah with equal zeal.
Now we can understand how a positive command overrides a prohibition. Indeed it is greater and the only reason why no punishment is mentioned is that the loss is infinite. This is why we must obey the command even if it means violating a prohibition (according to the rules and orders set out by halakha.)
Translations Courtesy of Sefaria, except when, sometimes, I disagree with the translation 
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