There often are quite a few corrections along the way for a 64-bit conversion. One way to set up the assembly part for your editor is on that Tools / Conf. User Tools... dialog, select the first -Empty- slot for hot key Ctrl+1. Then set the following, for example:
Menu Text: GoAsm x64
Command: C:\Program Files (x86)\GoTools\GoAsm.exe
Argument: /x64 $(FileTitle).asm
Initial Dir: $(FileDir)
Also select Capture Output, then OK.
From there, pressing Ctrl+1 will assemble the current file that you are working on in the editor (the above assumes a file extension of asm) and display the GoAsm output within the editor.
You can do similar for GoRC (build a RES file for linker) and GoLink on the next slots:
Menu Text: GoRC
Command: C:\Program Files (x86)\GoTools\GoRC.exe
Argument: /r $(FileTitle).rc
Initial Dir: $(FileDir)
Menu Text: GoLink
Command: C:\Program Files (x86)\GoTools\GoLink.exe
Argument: /debug coff $(FileTitle).obj $(FileTitle).res @Build.txt
Initial Dir: $(FileDir)
With the above method using FileTitle, a build could be as easy as Ctrl+1 Ctrl+2 Ctrl+3 (if you name your RC file with the same Title as the ASM one). Note that Build.txt is a text file in your project directory that contains other GoLink command line options and the list of import DLLs (or you can type these out in the Argument field instead).
Another way, it sounds like you have on your desktop either a batch file, or a short cut to one, that is specific to your current project. You can do similar to the above, by pointing to this batch file in the Command field, and clearing the Argument field (unless batch file does something useful here with arguments).
Something like the above should make it a bit easier without having to switch between windows.