Hi, I've been studying Japanese for ~3months, I've just started book #2. When I learn words and when I hear words in Japanese they "pop up" in my head in romaji. I know all hiragana and I could write/read them. Should I make the effort to imagine the words directly in Hiragana in my head or will that come automatically with some time, once I am more fluent in Hiragana?
Don't worry too much about which written version you start learning vocabulary in. As you mentioned, when you become more comfortable using hiragana, the transition will come along naturally. The most important thing is to focus on growing your overall Japanese vocabulary and to make sure your pronunciation is correct.