I have a Shimano Sustain 2500 reel.

 I would like to get a spare spool for ultra light flourocarbon applications, thus not needing a lot of line on there, nor a deep spool. Can I put a 1000 size school on this reel?

It will go on but the drag won't bite and the spool won't go up and down;making the handle hard to turn. So that's a no go. They sell shallow 2500 spools but they are not cheap. Like $100 or so I think. 

I go JDM with my spinning gear for that reason.  They make so many differen spools sizes and you can buy them individually.  I have both 2500S and 3000M spools for Shimanos.  

Yea I can find the spare 2500FG spools pretty easily but I figured maybe to use the 1000 series for ultralight line

19 minutes ago, Preytorien said:

Yea I can find the spare 2500FG spools pretty easily but I figured maybe to use the 1000 series for ultralight line

Just get a 2500 spool and put backer on it.  The only reel I don't have backer on is the shallow spool on my TwinPower.

If you were able to use the other spool you would have given up too much of your inches of line retrieved per turn.  Just get another correct spare spool for your reel. If you are concerned that the reel would hold too much really small diameter line then just fill the spare spool 1/2 full with 14 pound inexpensive but quality mono for backing. You can purchase a 1500 yard spool of Bass Pro Shops Excel mono for just $11.00. I used to fish with it. I now fill all of my reels with 1/2 a spool of Excel, and use a uni to uni knot. Tie a good quality arbor knot on first and make sure it can not slip on the spool. Spool it on tight and make sure it lays really nice and smooth. This allows the drag to work properly. Next use a uni to uni knot and tie on your more expensive ultralight fluorocarbon. I use the same technique to make expensive braid fill more than 1 reel, cutting the cost per reel fill up in half.  Doing it this way is both economical and effective. Only once have I had a fish pull the line out far enough for that double uni knot went out through the guides. I was striper fishing with rattle traps and a 18 pound blue cat almost spooled me before I could get the trolling motor up and the rod worked around the front of boat. I use the same double uni knot on rods I want to fish a leader on.