In the next few days I will be upgrading my iPhone 5s to a 6s I have a buyer for my 5s but would like to know how to save everything on my 5s and then wiping it to factory default before selling it ?

If you have a backup to either iTunes or iCloud you will be able to restore from that when setting up the new phone which will reproduce all the apps, settings, messages etc etc on the new device. You may want to run the backup manually one final time before setting the new phone up to make the backup as current as possible.

As far as wiping goes just go to settings/general/reset/erase all content and settings. You will need to enter your appleID and password before it will wipe to remove activation lock. Once erased it should be as new ready for your buyer

To to confirm connect to iTunes and click back up that will save all apps settings and everything else ?

Yeah it should do

If you're doing it through iTunes you'll need to connect the new phone when setting it up to restore the backup from iTunes

If you are already backing up to iCloud then it's easier to just use that.

So under the iCloud tab I have turned backup on and it's now doing it, how often does the phone back up and this is everything?

It will back up once every day when on charge. Yeah this backup will be everything and if you are backing up to iCloud you can just restore the new device from iCloud to restore everything to it.

You can manually perform a backup from the same tab to iCloud and as I said above you should do this before setting the new device up to make the backup as current as possible

Until you run out of iCloud space due to photos on the iPhone; then the choice is to turn off photo backup and back up everything else (my family do this as they send photos to shared photo stream and facebook) - or buy more storage from Apple (I do this).

iCloud 50GB storage is 79p a month.

If you're going to restore the backup to another phone, just make sure both phones are running the same iOS version.

This is true and if you are running iOS 9.3 public beta you will need to update the new device to the beta before restoring from backup

The OP won't be running a beta!

And don't forget to do this
https://support.apple.com/en-gb/HT201351