after posting the question I decided to do some research and now - a few hours later, I think I was able to put together a pretty comprehensive list to decide which goes where.
Before I start however, I'd like to warn you that - if you haven't already bought your caddy - there are two main form factors for caddies: 12,7mm and 9,5mm.. I obviously bought the wrong one... so make sure you get the proper size.
Physical considerations
SSDs are often thinner than normal 2,5" HDDs for obvious reasons. Dependent on how the disk is attached in the internal slot or in the caddy, you will always want the HDD to sit as tight as possible to prevent shocks and possible head crashes.
It may also be that the SSD or HDD due to its size only fits in one slot, forcing you to put the other disk into the other slot.
Compatability
There are user reports that they were unable to boot from the disk which was mounted in the ODD caddy. For performance reasons, you probably want the OS installed on the SDD, meaning that the SSD has to go into the interal, bootable slot. In rare occasions, the SSD may not even be recognized in the ODD bay.
performance differences
The SSD should always be installed in the slot with highest performance connector. I.e. in some occasions the ODD may use a IDE connector and the internal hard drive may be connected using SATA, in this case the SSD should go into the internal slot as well. When in doubt, the internal slot will be at least as good as the odd slot, if not better. Some notebooks may even have a SATA II connector for the ODD and a SATA III connector for the internal hdd
Hot-Swap capability
Some configurations allow hot-swapping the disk in the ODD bay, so if you are constantly switching drives between lets say your notebook and your pc, you would put that drive into the caddy and put the other disk in the internal slot.
aaand that covers about everything you need to know on that topic. If I have forgotten anything, please comment below. Otherwise have fun with your new fast speed notebook :)
Regards,
Xaser