I have few questions still, I want to know if connecting software wallet to your hardware wallet gives it the security as intended? If I start using software wallet on my hardware wallet does it add more to it's security? Or it's a bad idea?
You can't install any software wallet on your device, you can only connect them for transaction and address confirmation.
It's impossible to use your device without any software wallet.
What other things I need to look out for using my keynote hardware wallet?
What the heck is keynote hardware wallet?
Maybe you mean Keystone Pro 3 or something else??
As for the firmware update, I have two options, one through SD card and the second through USB connection, which one do you think is better and safer upgrade way?
USB firmware update is faster, with SD card it is slower but more secure because there is no internet connection.