You can do the upgrades in either order. All versions of CodeRunner (within the last few years, anyway) work with all versions of Jobe.
The caveat is that there might be a performance and/or disk-space hit with CodeRunner v3.6 (which I aim to release later this week) and a non-updated Jobe over time. It depends on how much use authors make of the new feature allowing students to attach files to their submission: what size files they allow, how many students, the amount of free disk space on Jobe and the file system it's using. If authors stay with the default file size limit of 10 kB, I wouldn't expect any problems with the old Jobe for months or even years.