Engine swap 85 to 88 Eagle

That's for the V-9 applications. I've never heard of a problem with the sixes in regards to cam gear.

What you DO need to watch for is oil pump binding. If the distributor doesn't bottom out on the block don't force it down with the hold-down clamp. Instead, get a washer or two large enough to go over the distributor body (may have to grind the washer a bit to fit against the block, and/or grind/file hole to fit). If you clamp it down the gears in the oil pump bind and can cause the pump or distributor shaft to shear or pump to seize.

I'm needing to jack up my 88 eagle wagon, and I want to use jack stands to hold up the car while I do some rust patching on the frame in the engine bay area, and brake and axle work. I'm concerned on the locations to put them. 

Here is where I normally place jackstands to support the front of the car - as I often don't want stands clear to the front interfering with jack placement or me sliding under the car.

Engine removal is best done from the bottom and don't even THINK about letting that front differential hang there on the axles like some have done. Some folks pull the engine and leave the differential hanging. Bad, very bad idea. Pull the differential and then the engine if you are doing the old "out the top" method, but with Eagles, it's a whole lot easier out the bottom!. Drop the whole bloody drive-train out the bottom onto dollies or something. You'll be glad you did.  NO wrestling at all, no fighting to get things to line up, no messing with bell housing bolts you can't get to, no fumbling with exhaust pipes and manifold nuts and studs and so on.
It's how the factory did it - up and in from the bottom. I put my engine/transmission/transfercase in by myself - with a ripped bicep in my left arm and I'm very left-handed, using the up and in from the bottom method.

Here in the circle is where I place jackstands. Just ahead of the rear cross member. I don't use blocks of wood because they can and will slip at times. I've watched it happen more than one time. Not on my cars as I have not done it that way, but the wood is a point of slippage. It also IMO negates the "ears" present on most decent stands which prevent sliding in at least 2 possible directions.
When I had the Eagle in the below photo on stands for this work I had 2 stands under the rear axle tubes and stands where indicated by the circle in the photo. To get the engine assembly out from under the car I placed a stout 4x4 across the front ends of the frame rails and hooked the chain from my gantry crane/chain hoist to the 4x4 and raised the car up high. Rear axle was on those stands, gantry crane holding up the front end so it was all pretty high in the air and I could slide/roll the engine out from under the car pretty easily. I then set the car back down on the stands, again where the circle is in the photo. All other work on the car was done with it on those 4 stands - the two under the rear differential axle tubes, and the fronts as shown.
To roll the car outside for pressure washing, I set a 4x4 across the bottom part of the gantry crane and let the car rest on that in the front, set the rear off the stands and simply pulled/pushed the car outside, pressure washed the engine bay, then pushed it back into my shop, raised it up again and set it on the stands.

AMC made several places they call jack points over the years. If it's fine for their cheap little jacks it's fine for a much more solid stand. Granted the Eagle uses bumper jacks, but the points are still there on these cars as they share a lot of the same body components.
I supported my cars from here since my very first AMC back in the early 1970s. Never had a slip, never bent or creased any sheet metal. The eagle is a pretty heavy car for AMC, comparatively speaking.
In this picture the line is where the rear cross member sits on the frame rails, the circle is roughly where I place stands.
Otherwise where the stands are shown in the other photo, up front near the front ends of the frame rails. Placement will depend on what you need clear access to and where your damaged areas are.
I use pretty decent quality stands - I don't trust my life and limb to stands from WalMart for $19.95.   I've got a full set of 4 heavy stands from NAPA and a pair my dad gave me a few years back when he quit crawling under cars and a pair I made when I needed to extend a Case tractor frame. (although the bulk of the tractor weight was on timbers, my stands supported the axle and some other parts)

As long as the car is stable it really doesn't matter where you put the jack stands. Obviously not in a thin area like directly under the floor, but on any of the braced areas, even the brace running under the seat. Under one of the sills ("frame rails") is best, but anywhere they aren't in your way and the surface is sound and sturdy is good. You mentioned working on rusted areas, so they might interfere with your work. Might be a good idea to place them furthest apart while removing the engine then jack the car up and move as needed when doing your rust repair. The car won't weigh near as much and weight distribution will change once the drivetrain is out.