1) Yes, assuming your OS X is install over UEFI. Create a new partition with MBR and install Windows on it, formatting it to NTFS then
2) No, you'll need Clover loader, otherwise your Hackintosh won't boot ...hence a LOADER. You could configure Clover to boot OS X after a set time but not remove the Clover interface during boot.
3) You probably have Clover theme set to random. You could download different themes and set it in the Config file or set it to Text Only under GUI.
4) Yes, you can upgrade to El Capitan directly like a real MAC, but make sure to install the latest Clover loader first, I suggest v3320 and up. Also make sure you have SIP disabled, you could add this in the Config file prior to upgrading.