Depending on your storage requirements, a single drive would always be faster, and more practical (e.g. no deciding which drive to use for what). You might compromise a small amount of storage, but using a single SSD instead of a SSD and HDD would be a cleaner approach.
Hi Rama930,
Intermittently detected drives can be caused by a faulting motherboard battery (e.g. CR2032) corrupting/losing the BIOS settings. Often replacing the battery, and updating the BIOS can fix this. Beyond this it is likely a bad drive controller or motherboard fault.
Hope this helps...