Should I use self-rising flour or all purpose flour for two ingredient pizza dough?
Self-rising flour is just flour with the addition of baking powder and salt*. So, it doesn't matter whether you use self-rising flour or make your own by combining these ingredients yourself. 

* note: not all countries include salt in self-rising flour. There is no salt added in the UK "self-raising" mixture for example, but there salt added in the US and Canada.

Because of this, if you live in the US and are using a UK recipe, you will need to omit some or all of the salt in the recipe since self-rising flour already contains salt. 

Conversely, if you are living in the UK and following a US recipe, you will need to add salt if using self-raising flour where it calls for self-rising flour. 

Otherwise you could end up with no salt or more than you intended. It sounds like in your case your recipe assumes that self-rising flour has salt added. 

One of our devoted readers also found that US self-rising flour has less baking powder than UK self-raising flour, raising doubts as to whether additional baking powder may be needed for some recipes. 

Note: A good clue will be the spelling of "self-raising" vs. "self-rising" to determine whether salt is expected in your mix. And Brits also have a lot of other weird spelling, grammar, and nomenclature differences, such as calling desserts "puddings." Be cautious when dealing with these people. They are very suspicious. 

In the end, I would suggest just using normal flour and adding salt and baking powder yourself. If you are using a recipe that calls for self-raising or self-rising or pulling-yourself-up-by-your-bootstraps flour, just find a similar recipe that calls for normal flour to see how much salt and baking powder should be used.