To reinforce what's been said, the focal length of a lens is determined when the lens is set to its infinity focus distance (furthest it can focus upon) and is a fixed value. A 50mm lens is 50mm no matter if its for a camera phone or a DSLR or a crop sensor DSLR or a medium format camera.
The difference between EF and EFS lenses is that the image circle (the image the lens produces behind it onto the sensor) is different. With an EFS lens the smaller sensor means that the image circle doesn't have to be as big, so the glass in the lens can also be smaller. This allows the lens to be smaller, lighter and cheaper than a comparable performing EF lens. Note that many EFS lenses still create a larger circle than they need and some can be mounted (with modification) to an EF body and produce quite a good image on the sensor. The edges will often be weaker performing (because your'e recording data from edges far outside of where the lens is intended to perform).
So yep if you got an EF 50mm and an EFS 50mm lens
On a Crop sensor body - they would give exactly the same photo.
On a Fullframe* sensor body - they would likely give exactly the same photo in the middle, but the EFS lens might have heavy vignetting (dark/black corners) and poorer performance on the edge, whilst the EF lens would cover the whole of the photo bright and clear and with good sharpness/detail.
That aside lets talk macro. With macro an important thing comes into play, the working distance. This is the distance between teh front of the lens and the subject. Not to be confused with the minimum focusing distance which is the distance from the sensor/film in the camera to the subject (which, thus, ignores the body of the lens). This is important in macro because you will often be at this closest point.
Most advise starting with a 100mm macro lens (or thereabouts) since it gives you a good working distance to play with. This makes lighting a lot easier because your body and camera are not overshadowing the subject and also means that if you work with subjects like insects you've a reduced chance of spooking them.
Macro lenses are also very high quality optics and performance from main and 3rd party brands is very broadly similar. So you've also got Sigmar, Tokina and Tamron to consider as viable alternative sources for macro lenses. This can let you get access to some great lenses like the Sigmar 150mm and 180mm macro lenses; a bit longer and thus giving you far more working distance. There's also neat affordable options like the very popular Tamron 90mm macro which is a very affordable and popular starting lens (difference between 100mm and 90mm in a practical sense isn't too great).
Derrel also mentions the background and this can be another confusing point for macro. Simply put the depth of field (region of the photo in focus and sharp) is identical no matter your focal length, assuming you use the same aperture. However a shorter focal length will blur the background regions far less than a longer focal length lens. Ergo that fade to a softer smoother background is greater on a longer focal length.
Now typically you won't see much difference unless you're comparing extremes. A 35mm macro compared to a 180mm macro will show this difference quite clearly, whilst comparing a 90mm to a 100mm you will hardly see it.
So you've pretty free choice for what to go for. Note that Canon has two 100mm macro lenses, the older which is a regular lens, and a newer which has IS. The optical performance for both is great, but the IS in the Canon is a new hybrid IS which not only counters side to side motion, but back and forward motion as well, which is something you contend with in macro and not other areas of photography**. This is a very neat boon, however be aware the majority of macro is done with manual focusing not AF (mostly because the back/forward motion would make it very inaccurate - so the canon lens helps out in this regard quite a lot, but its not essential for good macro photography).
*Note many EFS lenses protrude into the camera body a little when mounted, on an EF camera body if you were to modify the lens to fit, the rear of the lens can hit the front of the mirror as it flips up - damaging both. It's for this reason that Canon uses a different mount on the EFS so that it cannot mount to fullframe bodies. Note that most 3rd Partly lenses only use the EF mount so you have to be a little careful not mounting them to fullframe bodies if they are crop sensor lenses
** You set the lens to the focus you want and then move your body and lens into position, carefully squeezing the shutter so that you take the shot at the right moment. Your body sway and breathing will cause minor motions that you will see in the shot at macro distances. Support, good posture and a tripod can all help counter this. In regular photography these elements are not as much an issue because the motions are so slight they've got no effect