I have the sentence
彼はかなり英語が上手です。
Why is かなり in front of 英語, the noun, rather than the adjective 上手? Would there be any differences from the sentence above to this?
彼は英語がかなり上手です。
The natural position of an adverb of degree (程度{ていど}副詞{ふくし}) like かなり, とても, or 全然 is right before the adjective/verb it qualifies.
So there is absolutely nothing wrong with saying:
1) 息子さんがご飯をかなり食べましたね。
2) うちの部下も中国語がかなり上手いですよ。
this is the order you had in your second example.
However, by separating the 程度副詞 from its adjective/verb and placing it closer to the beginning of the sentence, as you did in your first example, you draw slightly more attention to it, and in effect emphasize it.
so by saying:
3) 息子さんがかなりご飯を食べましたね。
4) うちの部下もかなり中国語が上手いですよ。
it sounds like the son ate more food in 3 than in 1, and the subordinate sounds more proficient in Chinese in 4 than in 2.
However this difference is extremely slight in the vast majority of cases, and either is usually perfectly fine.
As a side note, a 程度副詞 qualifying another adverb MUST be directly before that adverb.
For example:
とてもゆっくりグラウンドを走った。makes sense, but
とてもグラウンドをゆっくり走った。sounds very odd.
however, both
グラウンドをとてもゆっくり走った。and
とてもゆっくりグラウンドを走った。are perfectly fine.