What’s the difference between a puja for a male deity and a puja for a female deity (such as Shiva/Durga)?

In my opinion, we all agree that there is one God/Goddess with a multitude of names. These names are indicative of the various attributes which we describe to God/Goddess. Even though, we know that She/He possesses them all.

Worshiping one form of deity, with a comprehensive list of attributes, it is easier to focus on our goals.

The attributes of each deity are represented by the stories of a divine image. Shiva is shown to be deeply meditative, with great renunciation. Durga or Chandi are known to be aggressively combating negative influences, clearing away obstacles.

Can one dedicate their life only to establishing one strong relationship with any one of the deities and their depth worship?

The worship of One deity will automatically lead to the worship of others. We will all find that when we find success in the pursuit of one type of attribute, we will automatically be drawn towards cultivating others. It will happen to each sadhu at his or her own pace, according to their karma and evolution.

Does worshipping the divine masculine and feminine help balance these sacred qualities and elements within oneself?

Worshipping both the masculine and feminine attributes gives us a much more well-rounded collection of qualities with which we understand the interaction with the world. It is like having a toolbox with only one tool, as compared to having many tools with which we can select the right tool for the right job. We can understand in which circumstances do we need to fight like Chandi, or close our eyes and meditate like Shiva. 

 Does one need a pantheon of Gods and Goddesses?

Ultimately, our image of divinity contains all the attributes of all the Gods and Goddesses. Where one God is present, they are all present in equal measure, with the exception that until and unless we are in samadhi, we tend to focus on one or a few attributes at any given time. In Samadhi we enjoy them all.