@benjaminparker the two actions different for the logic that is needed. Typically you would use a "run if" when you want to consider a particular condition and if true, do a set of things. The conditional action is more like a switch that operates the same, but does one or the other based on the condition being met.
It really comes down to how you want it to look in the designer more than anything, and also what you are attempting to evaluate as a condition. I have found some conditions work better in a run if, while others work better in a condition statement. Choice is yours, as long as it evaluates correctly. I have not seen a huge performance difference in either, because they both evaluate booleans at the end of the day.
Hope that helps.