No question, put them in as an assembly! Get them bolted together hanging in the air to make it soooo much easier to get the trans shaft aligned and fully inserted without damage and to get the bolts properly torqued. This makes it easier by far.
Drop it in starting out almost 90 deg to final position. As you lower it, twist it slightly getting the trans under the package shelf and it goes in easy as pie. The only thing to look for is there is a small boss on the block just in front of the oil filter that can catch on the cross member. Be aware of it when you think you only have to go another 2" to go. Wrap the trans in rags to protect finish.