I currently have a server with my girlfriend that is the crystal isles map but now we would like to change the map and bring some stuff with us. We plan to cryo dinos that we really want to keep and take some crafting stations that we recently made with us.  Can we upload our character with an inventory full of what we want to bring without losing anything?  Do we need to upload our items individually and then upload our character? 

As for clarification, we are renting one server.  We would like to change our current server to a new map, keeping all settings.  We want to bring dinos in cryo pods and some structures we have recently crafted. Whats the safest way to do this without losing anything?

The safest way would be to do this:
Choose a day to be a hardcore balls to the wall moving day.
On the day of moving:

Download all of your items to your Crystal Isles map.
Spin up a second server (At $18 a month, it will cost less than $1 to do this.)
Copy all of your settings using the new Copy Settings button to move your settings to the new server.
Cluster those servers using the new cluster tab (Shows up when you get two or more servers.)
Using the Obelisk, travel back and forth between the two servers to move the dinos, items, etc to the new server.
Once you're finished moving, download all the items to the new server, leaving nothing uploaded.
Make sure the survivors are on the new server.
Stop the old server.
Make a backup of the old server. (in case you want to spin it back up and start -right- where you left off.)
Download the backup of the old server, so you'll have a copy.
Delete the old server.

That is the safest way, and ensures no loss of data.

Anything else is taking chances that things will possibly corrupt.

The quick and dirty way:
Upload your stuff.
Change your map.
Reboot your server.
And hope ARK didn't ARK away your stuff.