'In way' is not the phrase here. This sentence says that you use 'something' 'in your emails' 'too often'. The 'in' is saying that the 'something' is in the emails the word 'way' is part of the phrase 'way too many', which means something is slightly past the instance of being 'just too many'.

I hope you are able to understand my answer and that it helps you. If not, then please reply to me and i will try again.

Another way to phrase this would be "Something you tend to use too much in your emails" or "Something you use in far too many if your emails" My take is that this sentence is a very informal way to speaking. As an example: "you say 'like' in WAAAAAY too many of your text messages". Emphasis in "way" is to show you're kind of annoyed, or it bothers you at whatever they say too much.