I usually just tap them in. If you make sure the axle end housing is clean they should "slide" in fairly easy, just mild resistance. Using the retainer to pull it in wouldn't be too bad for the last fraction, but if there's any significant resistance (burr, dirt, rocks, birds, little children, in the way) you don't want to force it and bend the retainer.
Mother's is a very good polish, so for aluminum that's already smooth and has been polished before it should work great. If the manifold is particularly dull or dirty it could take a lot of hand work to bring it back. Personally I prefer using a terry towel because you get more surface area and there are "nooks and crannies" for the waste paste to accumulate and still leave soft material to buff with, but have used the t shirt thing too with good results on anything that just needed a light polish.
