Yes, the rings you use should allow you to change the aperture. In terms of image quality with extension tubes, true macro lenses are probably the best, followed by primes, followed by zooms. Your zooms should give quite decent images, but they will not be as sharp as you'd get with a true macro lens.
Regarding the "real" aprture, adding extension tubes also increased the effective f/stop. Using a high aperture such as f/22 will give you better DOF, but at the expense of loss of detail due to diffraction. You will need to experiment a bit to see which apertures give you acceptable DOF with acceptable sharpness using your equipment.
When you are doing macro, focusing is usually done using slide rails, which move the camera back and forth. Depending on the magnification factor, and f/stop, you are dealing with DOF of a 0.5mm or even less, so everything about your setup has to be about minimizing unwanted movement. As well, you'll need LOTS of light so usually off-camera flashes are used to illuminate the subject. These also serve to keep the exposure short to minimize blurring due to movement.
When I do macro, the camera is on a sliding rail with focusing accomplished by turning a screw which moves the camera stage back and forth. The slide rail is sitting on a three-axis head, and that is on a very sturdy tripod. The lens is a macro lens set at a specific focusing distance (which determines the magnification). The subject is usually on a movable stage, also with micro-movement capabilities. The light is supplied by two flashes in manual mode, and I use a flash-meter to determine the right exposure. Although each flash has manual controls (adjustment of power from 1:1 to 1:128), you sometimes still have to fine-tune the light by moving the flashes closer or farther to achieve the correct balance. In addition, depending on the nature of the subject, you may need to use various light modifiers and diffusers, especially if the surface you are photographing is shiny. I've done my own sharpness tests, and have found that with my equipment, going above f/11 shows the loss of sharpness due to diffraction more and more.
For field work, magnifications above 1:1 are difficult because wind can make things move, the subjects you've shooting are moving about as well (assuming you're shooting insects), and you need a different strategy. I use a Manfrotto macro bracket that holds the two flashes aimed in the correct position, controlled by PC cables running out of an adaptor on the hotshoe. Whenever possible, the camera (and the associated bracket wth the flashes) will still be sitting on the focusing rail and rest of setup described earlier, and the focus, exposure, etc. are set in advance. Then I wait until my subject moves into view and press the shutter once it is in the correct position. However, it is very common to need to shoot lots of shots to get one or two that are acceptable from a composition point of view, even if you've nailed the exposure.