"I get shoes from my dad."
The に in a sentence with もらう markes the Person giving. Literally the "from" in "I am receiving shoes from my father".
Your second sentence should be: お父さんは僕にくつをあげる。 Dont forgett the さん. And the thing given by あげる is marked with an を. お父 without the san is not used.
And yes, you have to wrap your head around あげる、くれる and もらう. Took me ages as well. But its necessary to understand all three words.