Partitions don't necessarily matter, as you can split a drive into multiple logical partitions. Typically, though, you want your most demanding applications on the same physical drive as your OS. AFAIK, not having so incurs no "penalty", it's just that the application wont get the bonus of the SSD.
With SSDs, the best course of option is to know what you're putting on there. SSDs have finite write cycles (it's still years worth of writes). This is why I don't rememond that people install everything. Programs like WMP and even web browsers, don't really benefit all that much from the SSD, so you use a junction to make all of that moved over to the HDD. If you also offload things like the cache and temp files, you will make more space available on the SSD as well as increase its longevity.
TLDR version: make your HDD the default install location, but then use the SSD for your games and demanding apps. If possible, be selective of your MOST demanding apps to go onto the SSD, so you can have room for more of those apps.