No no no no no!
What you asked in your first post amounted to: "why is it wrong to do this:": y=\int\left ( c-\frac{1}{u} \right )du... the reason is because the LHS does not match the RHS ... you made a mistake evaluating the LHS.
If you want to do the RHS integration wrt u, you have more work ahead of you: I'll take it slowly this time...
Starting with:\frac{dy}{dx}=c-\frac{1}{u} I could rearrange that to be:dy = \left ( c-\frac{1}{u} \right )dx and then integrate:\int dy = \int \left ( c-\frac{1}{u} \right )dx... but how are you going to be able to do the integration on the RHS?
Well you could just put u=1+x^2 back!
But it looks like it is easier to integrate wrt u instead ...
What I did before was start at the beginning and use the chain rule:\frac{dy}{dx} = \frac{du}{dx}\frac{dy}{du} = c-\frac{1}{u}... now I can multiply both sides by du to give: \frac{du}{dx}dy = \left ( c-\frac{1}{u}\right ) du ... which is where I left you.
since we know that u=1+x2, we can find du/dx thus: \frac{du}{dx}=2x=2\sqrt{u-1} ... substitute it in:2\sqrt{u-1}dy = \left ( c-\frac{1}{u}\right ) du... I need all the expressions involving u in the RHS:dy = \left ( c-\frac{1}{u}\right ) \frac{du}{\sqrt{u-1}}... now you get to integrate:
y = \int \left ( c-\frac{1}{u}\right ) \frac{du}{\sqrt{u-1}}... which is left as an exercize for the student :)
Aside
... one of the powers of Liebnitz notation is that you can manipulate all the dx's and dy's and so on like fractions ... they obey the same rules. So, the chain rule amounts to saying:\frac{dy}{dx}=\frac{du}{du}\frac{dy}{dx}=\frac{du}{dx}\frac{dy}{du}... handy if you know u(x) but don't know y(x): it turns the problem of finding y(x) into that of finding y(u) ... which we hope will turn out to be easier.
You asked if we can always treat the du's and so on like this and the answer is "yes" ... if you are careful. eg.\int \frac{dy}{dx}dx = \int dy = y
Starting from \frac{dy}{dx}=c-\frac{1}{u} ... in order to be allowed to write an integration sign in front of an expression, the expression has to end in a d-something. eg. It makes no sense to write: y=\int x^2 ... it has to be y=\int x^2 dx and this had to start out as something like dy = x^2dx...
So let's apply that to the problem in hand ... we want to integrate the RHS with respect to u, but there is no du there. Solution: multiply the RHS by du. Whatever you do the the RHS you have to do to the LHS to balance the equation so:
\frac{dy}{dx}du=\left ( c-\frac{1}{u}\right ) du... that is all square for the RHS ... but what about the LHS? None of the dy, dx, du cancel out - but I notice that\frac{dy}{dx}du = \frac{dydu}{dx} = \frac{du}{dx}dy... you asked "can we always do that?" And there is your answer!