There is currently no way to utilize the "quantity" that is input by the user when adding a work assembly item to an estimate.
Ideally, there would be a special variable (similar to WAQty and EstQty) that would allow for the use of this quantity in the work assembly formulas.
Please review the following help topics:
https://help.sagecm.intacct.com/Content/Modules/Estimating/CostDatabase/WorkAssembly/WorkAssemblyOverview.htm
https://help.sagecm.intacct.com/Content/Modules/Estimating/CostDatabase/WorkAssembly/WorkAssemblySpecialVariables.htm
There is also a YouTube video, recorded using the old Corecon UI, but the information is still relevant: https://www.youtube.com/watch?v=L94jR87wicI&t=26s