Counters: what are you counting?
Japanese quantities usually use a counter suited to the item. A number's pronunciation can change with its counter, so learn the combination as a unit.
Choose a counter for the item
Use 人 for people, 冊 for books, and 枚 for thin, flat items. 本 means book as a noun, but as a counter it covers long items such as pencils and bottles. Do not choose a counter from the kanji's noun meaning alone.
The general counting forms ひとつ, ふたつ, and みっつ work for various things. They do not replace every specialized count, such as people or clock time, so also learn the usual counter for the situation.
Learn the sound changes
For people, 一人 is ひとり, 二人 is ふたり, 三人 is さんにん, and 四人 is よにん. Do not simply combine いち or に with the counter for the first two. Practice these four forms together.
本 changes sound in 一本（いっぽん）, 二本（にほん）, and 三本（さんぼん）; 六本 is ろっぽん. Listen separately for small っ and the endings ぽん, ぼん, and ほん rather than blurring them together.
Put the quantity into a sentence
りんごを三つ買いました。 means 'I bought three apples.' The quantity can appear before the verb. 三つのりんご instead forms a noun phrase meaning 'three apples.'
Ask いくつ for how many things, 何人（なんにん） for how many people, and 何冊（なんさつ） for how many books or volumes. Check that the counter in your answer matches what the question is counting.
Check: Should three books be counted as 三本?
Show the answer and why
Normally, use 三冊（さんさつ）. 本 means book as a noun, but its counter use covers long objects such as pencils and bottles.