Most of the game is played in real time, but the Plan and Go system is always available when you need it. In fact, if you keep forgetting to use the Command Mode, you can set various triggers in the options menu.
A good rule of thumb is to tap the spacebar anytime you are unsure of your situation. Once the game is paused, in Command Mode, you can scout the area and take all the time you need to plan the next step.
Early on, Command Mode will be very important for slowing down the action and allowing you to get familiar with line of sight and angles you need to hit your targets. As you progress, you may use it less but it is always a good idea to pop into Command Mode and survey a situation before launching a big attack.
When the number of enemies or the complexity of the situation increase, you should always use the Plan and Go system to coordinate assaults. The tactical advantages of using the Plan and Go system will become very apparent if you find yourself routinely getting ripped up in combat.
In those instances, go into Command Mode to verify your angles, accuracy, and damage while manually controlling your mercs.
The obvious trade off is that real-time action is faster and perhaps more exhilarating, while using Command Mode is slower and more methodical.
Like everything in life, there is a balance that needs to be had and if you find yourself doing poorly or proceeding too slowly, switch back a forth a bit more.