1. You can clone drive/partitions source as long as the total usage of that particular drive/partitions does not exceed the total size of the clone destination.
2. If you are using an SSD, try to leave at least around 10-15% storage space free, if you want your SSD to last long. Do not fill it to max.
3. Only programs and OS (Windows) will gain benefit, if you put them on SSD. Normal data e.g. music, videos, pictures, etc. however does not. You should move your normal data somewhere else, so it would not be part of the cloning.