Wheel size does make a very small difference, but it's really pretty small. With all other things equal the speed difference between 700's and 650's at the same rpm's is 10ths of a mile per hour. You will have to spin a little faster on 650s than 700s at the exact same gear ratio to maintain the exact same speed, but not by so much that it should be particularly noticeable and definitely not so much that you are spinning wildly - it's probably only around 5rpm difference. You can check it out here: http://velobase.com/Resource_Tools/GearCalc.aspx
I have both bikes with 650s and 700s. My 650 has standard double road gearing, the same as my 700. I can't say I notice any difference riding the two. The 650 is the heavier of the bikes, so it's actually faster on descents…