Suppose that you are involved in a woodworking project. There are two ways you could go about this project. First you could work on a single workbench bringing the tools to the project as you need them. Second you could take your project from tool to tool. In practice you are almost certain to do some combination of the two, and what combination you choose is largely dictated by physical constraints. It is not practical to carry a lathe to a dowel, nor would it make sense to drag a boat to a drill.
Vensim's Sketch Tools are like hand tools that you bring to your project. You pick one up by clicking on it, then take it to the spot on the sketch where you want to perform work. Vensim's Analysis Tools are like machinery that you take your project to. You pick up a piece of your project by selecting a variable into the workbench, then you click on the tool to perform the analysis.
This analogy is not perfect, but it is helpful in thinking about the function of the two sets of tools. In a typical woodworking shop you will have both a drill and a drill press. Both of these tools perform the same basic function, and yet you bring one to your work and you bring your work to the other. The Equation Editor can be used from both the Sketch Tools (acting as a drill) and the Analysis Tools (acting as a drill press).