Software interfaces for mathematical equation input usually require users to enter mathematical structures with nested components, for example, fractions or roots. The manner in which users interact with these interfaces has implications for future design decisions. In this paper, we examine the results of a study in which 14 novice mathematics users in an educational setting were video-recorded writing seven expressions each in two software interfaces: Microsoft Equation Editor (via Microsoft Word) and Mathematics Classroom Collaborator (MC2). Microsoft Equation Editor is ubiquitous and so default editor for many students, while MC2 allows for free-form input and so provides a comparison for how users might prefer to input mathematical structural elements. Extensive second-by-second coding was completed of the user's actions in the videos and Markov chain transition matrices were tabulated, estimating the transition probabilities for inputting structural elements, symbols, and operators under the two input models. This paper presents this analysis as well as a brief discussion of suggestions for mathematical software interface design.