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I would be purchasing the top end 3.7ghz model with the 2tb fusion drive, which I believe has a 128gb SSD.…

I will also need to run Windows through parallels for one piece of software.
Would I be able to run both windows and MacOS off the SSD portion of the fusion drive?
Windows through Parallels, yes, as long as the VM is small enough to fit entirely within those 128 GB along with macOS and your most-used apps. If your VM is under ~100 GB in size, it should be possible.

(Boot Camp, no. A Boot Camp partition will reside entirely on the spinning hard disk.)
since it does come with 128GB SSD how would that work..the mojave software goes on that and I can configure what software titles to go into the SSD drive, like final cut pro, motion, etc?
No, you can’t configure what goes where; macOS manages all that automatically. The OS will always reside on the SSD. As you run out of space on the SSD, your least-used apps and files will be moved, behind the scenes, to the spinning hard drive. You’ll rarely, if ever, notice it happening.

I’ve been using a 3TB Fusion Drive (at close to capacity!) for the past three and half years and have been delighted with its lightning-fast performance. I had no hesitation whatsoever in configuring my 2019 iMac with another 3TB Fusion Drive.

I posted my thoughts about Fusion Drives in a little more detail in another thread here. See also Ubele’s post here.
 
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