If you've got a mixed collection of 6.8SPC brass, you should sort out your cases based on the primer size. Hornady's brass is primed with small rifle primers, while Remington uses large rifle primers. However, if you really don't want to do this and your press is configured for large primers, I would just be extremely careful on the primer-seating stroke and, if resistance is encountered, remove the case for inspection. Set all the small-primer cases aside, then do them as a second batch.
At this moment, I am pretty confident that no one is doing Berdan-primed 6.8SPC, so that's not an issue at least.
Known Brands and Headstamps
Remington brass is stamped 'R-P' along the top of the headstamp. Large primers.
Although most companies use large primers, Hornady brass uses small primers.