Im still learning about adjusting shutter and aperture cohesively.

This is what I do:

Moving subjects - I use aperture priority (setting the aperture to what depth of field I want ie wide (2.8) = small DOF) and let the camera set speed (what you are calling shutter) and ISO. You can experiment with single shot or continuous shots depending on the speed of the subject - flying birds need continuous.

Stationary subjects

hand held - I use mostly manual mode, again nominating aperture depending on what DOF I require. I then adjust the ISO to ensure that the speed will be at least 2 x the focal length (example 100 mm focal length the speed should be around 1/200) when centering the exposure (on the exposure indicator in the viewfinder). Ensuring the speed is sufficient helps to ensure that you nail the focus.

tripod - here you can  lower the ISO to 100 and manually adjust speed and aperture to get enough light. If you want to smooth out water in the sea or waterfalls set it to speed priority, lower the speed (experiment) and let the camera do the rest.

There are other things you need to consider ie focus areas and modes

Look in my gallery if you want see how my pictures work out.

Strongly suggest you read something like:

http://www.amazon.com/Understanding-Exposure-Photographs-Digital-Updated/dp/0817463003