of course you can calculate conversion of yor process. Related of your second question, you have to be in mind that software respond to a set of conditions made by THE OPERATOR, At final of the simulation software is not responsible by the results. This responsability is of the operator, that, at the end has to check if the response is resonable ( for example, if there is a strange current composition, etc). So the type of reactor you should use depends of your reaction and the set of conditions you choose. I recommend to visit software manuals and some literature to see what kind of reactor people are choosing for the type of reaction you intend to use. Also I recommend you to check in the literature what kind of themodynamic model you will choose: it may influence your results.

in other words, simulation is a very and fast tool to study process, but you have to be sure what you want to sudy and set the themodynamical model and in the case the type of reactor to be helped by software.