Personally I use a gamepad on PC. I've always hated mouse and keyboard unless it's Starcraft or something. It's what I've grown up with and what I'm most comfortable with.

As far as when to use sic or obey, you should always use obey when in anything that matters; dungeons, primals, whatever. The good thing about obey is you only need to use it once and it will stay in obey mode until your egi dies or you resummon. Manually using abilities with your egi is pretty simple, it just takes practice using them at the right time. The neat thing about using the abilities is that if your egi is currently attacking an enemy and you command it to use, say, landslide on a second target, it will use landslide on the second target and return to attacking it's primary target. I learned this messing around in Mor Dhona.

It'd be good to take time to learn the place and heel commands as well. These help immensely with some fights and can save you a lot of work keeping your egi alive.