I'm not sure why they say image quality will degrade. There is nothing but air inside the extension tubes - all you lose is a few stops of light. Possibly some vignetting (darkened corners). 50mm worth of extension is certainly a reasonable amount to use.

You will have a very shallow depth of field, and very little latitude to focus with the lens itself, rather you move the camera closer/further from the subject to focus. With the shallow depth of field, it is very hard to get close, in focus and hold the camera steady to get a shot, so you'll want to use a tripod if possible.

It is normal that the subject distance will have to be very close to use the extension tubes - that's really the whole point - the extension tubes allow you to move the lens and focus much closer to the subject, to get more magnification.

Edit: now that you've added that you are using a 100mm lens, there is something else to consider. The magnification you'll get from adding extension tubes is the length of the extension tubes divided by the focal length of the lens. So if you use your two 25mm tubes with a 50mm prime lens, you'd get 50mm / 50mm = 1:1 ratio. If you use them with the 100mm lens, it's 50mm/100mm = 1:2 ratio - that's half the magnification you'd get from using them with the 50mm lens. The macro lens combination might be partially compensated by the fact that it may focus closer (and because the macro lens may have an effective focal length of only 70mm or so when at closest focus). So experiment if you have a 35mm or 50mm lens - you may actually get better results than using the tubes with the 100mm.