I can't swear to the later models, but I'm sure that the AMC six had a two-piece seal all the way up (from inception to 2007.)
Every aftermarket seal I've seen has had the "ears" on one half, and they're there to ensure that the two halves seal against each other. The channel in the rear main cap and/or the engine block should accommodate them, so it should be no trouble. Leave them on.
Also note that the seal halves will probably protrude slightly when installed properly - this is also intentional. The "crush" this provides also helps to seal the two halves against each other.
Pay careful attention to orientation on installation - the "open" side of the V (you'll know it when you see it) should be toward the inside of the engine. If you reverse it, it will leak! Also, take a moment to run your thumbnail front-to-back (or back-to-front) at several locations on the rear main sealing surface on the crankshaft. If you feel a "hitch" or a "grab" doing so, you may have a groove worn into your crankshaft - and the new seal will leak. This is not the fault of the seal - the groove would be worn in by grit caught under the old seal, and the new seal lip won't contact the surface all the way. There are a few solutions here:
1) Get a double-lip seal (easiest) or an offset-lip seal (I know these exist, but not for all applications.)
2) Locate and purchase a repair sleeve (requires partial or total crankshaft removal to install.)
3) Remove the crankshaft and replace it outright, or take yours to a crank shop and have it welded and ground (most difficult, and spendy.)
When I say "partial" removal, I'm referring to loosening the front main caps, removing the rearward ones, and getting yourself 1/4" or so of daylight over the rear main sealing journal so you have room to install the seal. If you're careful, this will work - if you're quick, you don't have to worry about warping the crank. Note that you usually have to heat up the sleeve to expand it, tap it into place, and allow it to cool for a shrink-fit. I've used these in various applications - follow the instructions, and the thing will work!
I mention checking for the groove now because I've run across jobs where someone has said "I changed the RMS twice, and the damn thing still leaks. What am I doing wrong?" At least they asked the right question - not checking means you're doing something wrong... Anytime you change a wiper seal, you always want to check the surface where the seal lip rides! Anywhere.