Yes, there's a big difference. そうですね as a conversation filler sounds more intimate, and it's usually used to agree with what the other is saying.
On the other hand, そうですか is often used to let the other known that you've undederstood so far what the other has said, but this doesn't mean he accepted or agreed with him. Even to show disagreement on the other's remark (when the intonation is rising!).
But note that the meaning of these "conversation fillers" depend largely on their intonation. I've written that そうですね is more intimate, but it can be a sign of indifference when it's said lifelessly, uncaringly.
Also note that you should use these conversation fillers sparingly; otherwise you sound tacky or the conversation becomes awkward. ええ、はい are more frequently used.
そうですね
そうですか