I want to clean install OS X (El Capitan) on my MacBook Pro with two internal hard drives
Answer to Question 1.

The only way to know for sure is for you to edit your answer and post the output from the commands below.

sudo  fdisk  /dev/disk0
sudo  fdisk  /dev/disk1


These commands will not change your computer. What I am looking for is a small partition on the SSD that can be used to boot Windows. Most likely you don't have this partition, which would mean you are booting Windows entirely from your HDD. Anyway, this is the only way to know the answer for sure.

Answer to Question 2.

I am not sure how to plan to clone a Windows partition. Personally, I use Winclone which is not free software. The OS X partition can be cloned using the Disk Utility. You can also save your files to a .dmg file on an external disk.  My preference would be to put the old drive in a USB enclosure. You then could not only boot OSX from this drive via the USB port, but you can copy necessary files back to your new internal SSD. As for using Time Machine, it has never been my choice, but other seem to prefer using it. 

Answer to Question 3.

Same as question 1. Depends on how your disks are partitioned. If you do end up recreating Windows from scratch, how do you intend to do that? You no longer have a optical drive.

I will assume before doing anything, you have created a copy of your recovery partition to a USB flash drive. That way if every goes wrong, at least you can  boot from the flash drive and download Yosemite.