The CD input on most amps doesn't use the pre-amp section or EQ, it's just fed to the last part of the amplification and in to the speaker at maximum volume.
What that means is that you'll have to change the volume of the feeding signal from amplitube. So in essence you will be using only the speaker of your bass amp.
Some info, the RCA cables are unbalanced which means you'll have to cope with -6db output.
The Amp gets Hi-Z signal from the instrument and is designed to work that way.
I don't want to get too technical about it but it concerns impedance and levels as said before.
Now if you really want to integrate your bass amp with your scarlett the signal flow goes like this:
1.Bass Guitar -> 2.Scarlet 2i4 Instrument input -> 3.Amplitube -> 4.Balanced monitor output (left or right) -> 5.Re-amp Box (http://www.radialeng.com/prormp.php) -> 6.Bass Amp
so about step 4: Your scarlett has 2 outputs that feed signal into your monitor setup, These are balanced connections and feed line signal to your Active monitors. You can configure from your DAW the output of the amplitube channel to be one of these two outputs, So to do this right you'll have to "sacrifice" stereo monitoring , feed the whole mix to the one channel (if you are doing it for recording purposes) and reamp the other channel.
If you want to keep sending from your RCA channel i would recommend before you go to your re-amp box to use an Unbalanced To Balanced signal converter
(http://www.bswusa.com/Hum-Reduction-Rolls-BUZZOFF-P4661.aspx) This will make a much healthier signal to feed into the amp, but costs some money too.
So What you are after is a reamping process as Johannes stated before, either you record it afterwards or not.You can find countless posts concerning this matter on the internet.
Also one matter you must have figured out by now is the latency of your card.