Yeah, you seem to be on a pretty good track here. Most people who attempt learn that usually have more mathematical experience, so some things seem to them more natural than to you, e.g.:
> Finally, I have a vague understanding that a scheme is the result of gluing some affine schemes together. Sheaf stuff is involved.
For most mathematicians, this step is actually rather clear, because the intuition here is that "you glue schemes from affine schemes same way you glue (topological/differential) manifolds from pieces that look like R^n", and people studying mathematics typically have extensive experience with manifolds before they encounter schemes.
> and in the category of affine schemes it becomes an equaliser, and equalisers on "spaces" are supposed to form subsets somehow.
The intuition here is something like this: let's assume that R is algebraically closed, for example let R = C, ring of complex numbers. Then C[x, y] is a ring of polynomial functions defined on complex space C^2, and C[x, y]/(x^2 + y^2 - 1) is a ring of polynomial functions defined on the subspace V = { x^2 + y^2 - 1 = 0 }: if you have two functions f, g \in C[x, y], such that f(z) = g(z) for all z in V, then function h = f - g must be zero on the entire V, so (by Hilbert's Nullstellensatz), h must be in the ideal (x^2 + y^2 - 1). So, two elements f, g of C[x, y] restrict to the same function on V = { x^2 + y^2 - 1 = 0 } precisely when their difference is in the ideal I = (x^2 + y^2 - 1), so the ring of functions on V is exactly the quotient ring C[x, y]/I (or, as you call it, equalizer, which is correct, but it's never called this way by geometers).
> I have no idea how you compute with this, especially given how elaborate the definitions are.
Let me give you an example that I found very illuminating, which just so happen to talk about the scheme Spec(R[X,Y]/(X^2 + Y^2 - 1)) you mentioned: see section "6.5.8. More examples of rational maps." in http://math.stanford.edu/~vakil/216blog/FOAGnov1817public.pd...