To solve the centers I begin by picking a color. I find that center and make a 1x2 block by moving a piece next to it. I
hold the cube so that these are on the Top. Next I move pieces around the lower layers and create another 1x2 block which
I will move next to the block already on the Top face. I repeat this again until I have a 3x2 block on Top. Lastly I arrange
the remaining pieces into a 1x3 block and move that to the Top to complete the center. If you have pieces on the Bottom,
try to rotate the Top so it is out of the way when you rotate the l or r layers to move it to a side adjacent to the top.
Now pick your next color and form a 1x2 block. You shouldn't have to worry about messing up the Top or Bottom centers and you don't need to move the l or r slices to complete the remaining centers. After completing a 1x2 block I rotate it so that the d layer is clear to move around (i.e. the 1x2 block is above it). That allows me to move other pieces through the d layer without disturbing what I already have. You should be able to complete your third center without any problem.
When moving on to the fourth center you should not solve the side opposite from your third center. If you do, then the last two centers will be on opposite sites and that makes it much more difficult to complete (in my opinion).
Unlike the 4x4x4, I don't have an algorithm to move pieces around until the last two centers. Just keep following the same method as above, creating 1x2 blocks and moving them into place. Once you get to the last 2 centers you may find it difficult to move the last few pieces into place. Depending on whether you need to move in a 'corner' or 'edge' piece for the center you can use one of the 2 methods shown below. Moving a corner piece into place usually results in a need to move in an edge. The examples below show first how to get the corners correct and then how to move the last piece into place.
If you have more than one corner or edge piece out of place you can repeat the algorithms above. Just be sure to put all the corners into place first, then the edges.
You should be all done with the centers now and ready to proceed to Solving the Edges.