By "flowchart", I presume you mean "project flow". The issue of execution sequence was discussed here with Chris H a couple of months ago, and there is a disagreement between the Project designer and Project explorer. The designer allows you to drag and drop queries, and I think the explorer does as well, but for execution sequence they don't always agree. My solution to this some time ago was to specify the execution sequence with explicit links and then drag the queries around so they represented the link sequence. In that way you can define a new query and move it wherever you want it in the sequence.
I need to ask though why you want to do this. Have you decided that the output of Query A is to go through some other process before going through Query process B? Or do you simply want to add another analysis task to report on your data? If you're just reporting on the data, then the sequence is probably irrelevant. Otherwise you'll need to work with the project designer.
I'm sorry if any of this is vague, my metadata server has decided to be difficult again this morning, and I am writing from memory.
The answer depends on what the elements are. Let's say for the sake of example they are a data set and a bar chart task -- the bar chart uses the data as input.
To insert a query in the middle, first right-click on the data and select Filter and Query. Design the query as you want and run it.
This creates another data node -- the output from the query.
Right-click on the bar chart node in the process flow and click Select Input Data, selecting the new data output table you just created (don't select the query itself -- that's the one with the little filter in the icon).
Result: the process flow redraws with the query and its output in between the original input data and the bar chart. Rerunning the bar chart will pick up the new input.