All example code for the methods have it placed in setup(), and I have not had any luck placing them into loop(). I want my arduino to be able to run code while passively checking for requests, is there a workaround if this is the situation? Thanks!
They are not commands!
Yes you can use them in loop() - there is no situation other than you doing something wrong.
The fault is all yours.
Mark
Do you mean "Wire.begin()"? Typically each library has a "begin()" method that is called once before doing anything else with the library. Since it is only needed once it is typically put in setup().
The 'master' device initiates all transactions. You can't "passively check for requests" unless you are a 'slave' device. When a request comes in the handler you set in 'Wire.onReceive()' gets called. See the "slave_receiver" example.