How to write in Hiragana and Kanji?

I'm learning how to read and write Japanese, and I'm writing out sentences on my iPhone using the Romaji keyboard.
Everytime I write a sentence, it pops up in a bar right below, but it shows different characters sometimes. Like every character will be the same as I wrote, but one or two, maybe more, will be huge and different.
I did some research and I found that this is Kanji, and that the common Japanese writing system is Hiragana.
I'm confused! Should I keep the Kanji in my sentences, or should I ignore it and continue writing the sentence in Hiragana? Does it make a difference in the translation/meaning? Should I keep it Hiragana if I want to?

Japanese adults use both hiragana and kanji in their writing, so the program automatically changes the hiragana that would be written as kanji into kanji. Kanji helps to clarify the meaning of same-sounding words.

Only children write without using kanji in Japan. If you know the characters I suggest you use them.

Kanji is main part of Japanese. Many nouns, verb stems, and adjective stems along with names and locations are all written in Kanji.

I suggest you learn the hiragana first and then identify its kanji.