The growing popularity of biochemical genealogy places greater emphasis on the distinctions among data, information and evidence. (See also What is the difference between evidence and information?).
As you have noted, the test provider will return a vast array of data which may or may not be relevant to your current needs (or to your future interests in further investigation). In its raw form, this has little or no value in a genealogical sense. Note also, that the data set you receive will depend upon the choice of tests you had carried out (but more on that later).
Depending upon the test package you have purchased, some of that data will be distilled into information that the provider believes is relevant to your situation. Since most FH software gives you the facility to store {label, value} pairs, you should certainly store that information until you decide what it means to you.
If you have been corresponding with a possible (male) cousin about your (presumed) great grandfather, then two pieces of information about Y-chromosome markers (yours and his) can constitute evidence for the link between your family trees. When you combine the trees, you will cite the DNA test as justification (or, at least, support) for your decision.
At the present time, few family historians understand the type of generic information that is required as evidence for particular problems we face. DNA test providers have tended to concentrate on delivering as much information as possible rather than ensuring they understand what clients actually need.
Would you walk into a vital records registry and ask to purchase certificates for all the Smith births in the nineteenth century? For some of us, getting a DNA test is rather like that. We need to become more sophisticated clients and learn to frame our information requests to match our needs rather than the providers stock.
Begin with the genealogical question that interests you ("Is it true that we have spanish ancestry?") only then can you find out what type of genetic information can provide evidence relevant to that question. Then look within the mass of data provided for information (in this case, on haplogroups) to be recorded as evidence for or against the family legend.
As with most family history searches, the ideal is to understand the question before you start to gather information; although we all have boxes of documents that may or may not be useful. If your aim is to identify a candidate father of an ancestor, then using a mitochonrial DNA test will be a waste of time and money (for that particular question) because the information it will provide cannot constitute evidence. Think of it as being like obtaining a birth certificate in order to identify the cause of death -- all the information is true and concerns the right person, but is useless for the intended purpose.
Every new data type requires us to learn when and how to interrogate it in order to obtain value for our purposes. Biochemical tools are opening up new opportunities, but they will demand study.