Let's start with a word of caution: on the internet, the terms macroevolution and microevolution (especially together) are usually used primarily in creationist rhetoric. As such, it is usually best to avoid them, especially when talking to a lay audience. The main mistake creationists perpetuate when thinking about micro-vs-macro evolution, is that the two are somehow different and distinct physical processes. This is simply not the case, they are both just evolution. The scientific distinction between the terms, comes not from the physical world around us, but from how we choose to talk about it. When a biologist says "microevolution" or "macroevolution" they are actually signaling what kind of questions they are interested in asking, or what sort of tools they plan on using.
Verbal and empirical theories
In verbal and empirical theories, the micro-macro distinction is usually one of timescales. A person in the macroevolutionary paradigm, usually asks questions above the level of individual species, as Evolution 101 writes (emphasis mine):
instead of focusing on an individual beetle species, a macroevolutionary lens might require that we zoom out on the tree of life, to assess the diversity of the entire beetle clade and its position on the tree.
Empirically, macroevolutionary answers to these sort of questions are usually ones that don't have access to detailed evolutionary histories or direct experiment. Instead, the method tends to be ones that use geology, fossils, and back-inferences from broad differences/similarities of existing species. As such, most macroevolutionary theories tend to be descriptive, instead of predictive. Most of paleontology can be classified under the macroevolutionary paradigm.
If someone explicitly says that they are looking at microevolution then this usually refers to a contrasting methodology that tends to be heavy on direct experimental manipulation. Most importantly, microevolutionists tend to have access to rich and detailed evolutionary histories. As such, it is not surprising that you saw a study that identified itself as microevolutionary while looking at different species of Drosophila. The fruit fly is one of the widest used model organisms, and as such the study you are referring to probably experimentally manipulated populations of fruit flies and collected a rich dataset of genetic changes in the generations of fruit flies that they studied.
Of course, most studies are at intermittent levels, and no this isn't called meso-evolution (except by silly people). If you are not clearly using the macroevolutionary nor the microevolutionary paradigm but still looking at evolution, you would just simply say 'evolutionary' without any prefix.
Formal and mathematical models
For formal and mathematical theories, the micro/macro distinction is also one of methods used by the theorist not of the underlying domain they are studying. Mathematical modeling of evolution falls into two broad categories: frequency-dependent and frequency-independent models. Frequency-dependent models almost never make the micro-macro distinction. Although you could argue that dynamic models in evolutionary game theory are micro, and static equilibrium concepts like ESS are macro, but I doubt theorists would endorse this view. As such, I will focus on the frequency-independent models.
For frequency-independent models, they key concept is the fitness landscape -- a way to map each genotype to a fitness. If the model tracks a population (a distribution over vertices in the fitness graph) on a static fitness landscape, then it would typically be just called an evolutionary model (the word microevolutionary is seldom used explicitly in this field). However, if the authors assume that mutations are extremely rare and thus any mutant goes to fixation before a new one arises then they can use Gillespie (1983, 1984) to replace the population by a single "typical individual" occupying one vertex of the fitness graph. At this point, the model becomes macroevolutionary and the underlying rule for calculating fixation probabilities would be the microevolutionary component. This approach is often also coupled with an alternation of change in fitness landscape followed by mutations and a selective sweep. Fundamentally, though, macroevolutionary models are just convenient (or tractable) approximations to a real underlying evolutionary dynamics. This should never be forgotten.
Strange example bridging the gaps
Finally, it is important to stress that the macro- and micro-evolutionary paradigms are not necessarily exclusive and do not have to correspond to a difference in timescales! This is best done with an example of a respected theoretical study that mixes everything together. Kauffman & Weinberger (1989) used their newly developed NK model or rugged fitness landscapes to study maturation of the immune response (Tonegawa, 1983). The developed a macroevolutionary mathematical model because they used Gillespie's trick to replace a population by a typical individual by abstracting away from the underlying microevolutionary calculation of fixation probabilities. However, their model was studying evolutionary dynamics within the human immune system (so timescales of days to weeks) and was tuned by parameters gathered by empirical microevolutionary studies that tracked individual nucleotide changes (Crews et al., 1981; Tonegawa, 1983; Clark et al., 1985). Lastly, the study results can be used to inform a question typical of verbal macroevolutionary theory: Are there any examples of sudden leaps in evolution?.
As such, the above study used a formal macroevolutionary model, informed by empirical microevolutionary work, to help us understand a question typical of verbal macroevolution while looking at a physical process that operated on the incredibly short timescale of days to weeks. No wonder people are so confused by the micro-macro "divide"!
References
Clark, S.H., Huppi, K., Ruezinsky, D., Staudt, L., Gerhard, W., & Weigert, M. (1985). Inter- and intraclonal diversity in the antibody response to influenza hemagglutin. J. Exp. Med. 161, 687.
Crews, S., Griffin, J., Huang, H., Calame, K., & Hood, L. (1981). A single V gene segment encodes the immune response to phosphorylcholine: somatic mutation is correlated with the class of the antibody. Cell 25, 59.
Gillespie, J.H. (1983). A simple stochastic gene substitution model. Theor. Pop. Biol. 23, 202.
Gillespie, J.H. (1984). Molecular evolution over the mutational landscape. Evolution 38, 1116.
Kauffman, S. and Weinberger, E. (1989) The NK Model of rugged fitness landscapes and its application to the maturation of the immune response. Journal of Theoretical Biology, 141(2): 211-245
Tonegawa, S. (1983). Somatic generation of antibody diversity. Nature 302, 575.
