I was never allowed to do things the way I wanted to do them.
We have to make it work in the way that we want it to.
What's the difference between "the way" and "in the way"?
When should I use "the way" and when should I use "in the way"?
To stay clear, I'd prefer not to use in the way because it also means an impediment i.e. something coming in between. Using this phrase would imply its use more as an idiom.
"I cannot dance because the table is in the way."
Hence, to avoid its idiomatic use, in those sentences, I'd prefer using the way.
Use in the way if you want to convey that something comes in between and prefer ...the way... that would convey the message without any ambiguity.
It makes no difference whether you use "the way" or "in the way" in the contexts of the two sentences presented. But the use of the former is much more idiomatic and preferable. Besides, "the way" and "in the way" aren't always interchangeable; their use depends on the context.
'the way' is an idiomatic phrase, according to The Free Dictionary, that means "in the manner that". So if you use "the way" in these sentences, its use makes sense that's correct grammatically.
However, if you use 'the way' to mean 'the manner', you can rephrase these sentences as follows:
I was never allowed to do things the way that I wanted to do them.
We have to make it work the way that we want it to.
The 'that' has been used here to mean 'in which". We can use the that to mean in, on, by, or with which (The Free Dictionary).
You can also say:
I was never allowed to do things the way in which I wanted to do them
We have to make it work the way in which we want it to.
Look at the following sentences in which the use of "in the way" isn't possible.
I like the way she dresses.
I hate the way she always criticizes me.
Look at another example in which "the way" instead of "in the way" isn't possible:
I take pride in the way my son helps the poor.
So the use of "the way" and "in the way" depends on the context of a sentence. Besides, where they can be interchanged, the use of "the way" is much more common and idiomatic.