I am new to Japanese. I wanted to know what are the tools used for typing Japanese (specifically desktop typing, not mobile). Phonetic tools are always available to type languages, but are there any preferred tools over the phonetic ones? I want to start acquiring skilled and professional Japanese typing.
I'm going to go a bit more broad with answering that kandyman did.
In general, these are called IMEs. This is software you use to actually translate what is commonly seen as Romaji into actual Hiragana, Katakana or Kanji.
I won't make any recommendations since that's not really my intention here, but I will say this:
Using an IME does not mean you're now able to proficiently type Japanese.
Converting between Kanji, Hiragana and Katakana is a many-to-many match, and while most common phrases and expressions may be filled in, you have to know and understand the context of what characters are actually being displayed on-screen. Otherwise, what you're typing will be confusing or indiscernible to someone else.
It's the difference between typing 間に合いそう (let's make it on time) or マニアイソ (mania).
This seems like a question for the Meta Stack Exchange, but I think you are just asking about input methods, right?
If you just mean basic input, then you need to install a Japanese Input Method - instructions here.
This article will explain it in more detail, but if you just want to get started quickly, then install the MS-IME on your computer and select romaji as the input method. Then you can type a word like にほんご by typing the combinations
ni ho nn go on your qwerty keyboard.