This is a Frequently Asked Question...
Short answer: Sage may transform the expressions for you (e.g.: factor, expand, simplify, as well as specialized transforms such as trig_reduce or canonicalize_radical), but you don't have control of the exact form. This is determined by Sage's (often Maxima's) heuristics. Since there is no algorithmic definition of the "right" form, your taste may clash with Sage's developer's...
sage: E=b-a
sage: E
-a + b
is indeed annoying. But you may see better by asking:
sage: -E
a - b
Similarly, you can take advantage of Sage's abilities to transform expressions to do, for example, "intelligent checks". For example, you can isolate various parts of an expression by using coeffocients, to get subexpressions easier to check. Imagine you want to check some trig expression: such as:
sage: sin(13*x).trig_expand()
13*cos(x)^12*sin(x) - 286*cos(x)^10*sin(x)^3 + 1287*cos(x)^8*sin(x)^5 - 1716*cos(x)^6*sin(x)^7 + 715*cos(x)^4*sin(x)^9 - 78*cos(x)^2*sin(x)^11 + sin(x)^13
To check this, it might be easier to ask for:
sage: sin(13*x).trig_expand().coefficients(sin(x))
[[13*cos(x)^12, 1],
[-286*cos(x)^10, 3],
[1287*cos(x)^8, 5],
[-1716*cos(x)^6, 7],
[715*cos(x)^4, 9],
[-78*cos(x)^2, 11],
[1, 13]]
which is, arguably, easier to understand and check... You can also reverse your transformations in order to check that you get your original expression back:
sage: sin(13*x).trig_expand().trig_reduce()
sin(13*x)
A frequent application is deriving a difficult-to-obtain antiderivative (should be mandatory, IMHO...). Similarly, numerical integration can be used to check a suspicious definite integration ; in the same vein, graphics can be helpful...
Another direction is to try and find common subexpressions and replacing them by short symbolic names. Look for cse in sympy, which can be of help...
