It seems that I am liking this game

Oh. Ottoman Empire and it's allies. DOOOOM when playing as Greece. I miss old EU3 times. Where Christian nations never ally to Muslim ones. And no, if you make a country your puppet it's not automatically in your SoI. You have to do it manually.

Good to hear you enjoying the game =)

The puppeting vs sphering one was a question that confused me at first. Basically, the difference is a puppet will always support you military wise if you ask them and another nation cannot communicate with them (only through you).

Sphering is slightly different, they will still support you in wars if you request they do so, however they can communicate with other countries. The big bonus of sphering is the economical one - they will buy / sell to you first over other nations - this does not happen with puppeting.

A lot of people don't seen to be fans of puppeting... I personally love it, I puppet then I sphere them. It's a lot less micromanaging as other nations seems less inclined to attempt to take it out of your sphere if they are your puppet (not confirmed, just my experience.)

Also, the reason I opt for puppeting is my economy generally rocks anyway and as I focus on military and thus have a high prestige, I rarely have trouble getting goods (the national with a higher prestige always buys first, so if two competing nations are trying to purchase goods and there is a shortage, the one with the highest prestige purchases first)

Never puppet anything ever. Puppets are useless. It doesn't take a lot of thinking to realise that, since you can't puppet GPs, then you can only have puppets that are, at best, secondary powers. What exactly is the point in having a puppet that will lose battles and occupation warscore for you? Spherelings will always join your battles if you want them to (you don't want them to, most of the time, but it doesn't matter), but they'll also help your economy a great deal. Are you really going to spend 11 infamy to reduce your military strength?

I think that really depends on the country's circumstances moldeh. Playing as China I knew I would be hosed if several of my substates were sphered and my nations combined military power was fractured, so by using less infamy I could force other nations to submit their sovereignty to my control. That way no one great power had enough influence to force enough my other subjects out of a war when the time came - or atleast making it considerably more difficult. Makes for a reasonable deterrance from that perspective.