There are lots of ways you can do this. Who's invoking the first copy of wyUpdate (is it within your program, or is a user doing it, or can it be either)? If it's always your program that's launching the first copy of wyUpdate, then you can just write it to wait for the first one to finish sucessfully then launch the next one.
Another option is to create a simple *.bat file, include it in the "Temporary files" folder in wyBuild, and have it execute wyUpdate. (see: Executing files in your update).
It all really depends on what you want to do and how you want to go about it.