@henleyjj Only 1 uplink from each switch in the stack will be active at one time, but you can link both to both as you have suggested.
We originally set up all of our sites with only one link to each MX and then started adding a second, but stopped as it did create some spanning-tree issues where we had MS and MX. Therefore on the dual linked sites we commonly left the second link port disabled, so it could be activated in an emergency, but wouldn't stop the switches coming back up after a reboot. This has since been resolved but we have left it as it is with some single linked and some dual linked...!
The sites that had Cisco IOS switch stacks with MX were fine.
The only issue that you might experience with the single linked option is that if one switch went down, you could end up with the MXs operating in dual master mode and you don't want that.