The interaction between MeasureSquare and JobRunner is really very simple. In MeasureSquare, the file is exported as a FSDE file.
Step 1: In MeasureSquare Click on File> Export MeasureSquare Report> Export FSDE File.
Step 2: In JobRunner, on the new Proposal screen, the user clicks on the "Takeoff" button and selects MeasureSquare. Locate the FSDE file and Import. Basically there are only 4 fields importing: Qty, UOM, Description, and Color.
I'd recommend printing one page of the MeasureSquare, export just that one page, import into the JobRunner system and do a side-by-side comparison to see which fields are mapping to where.