In my experience it is very important to use the same wood for the floating tennon as the pieces which you are putting together. Assuming you are assembling a 90 deg. joint the tennon will be long grain to long grain with one member and long grain to cross grain with the other. You want to minimize differential rates of expansion/contraction with seasonal changes so using the same wood is the best way to insure that. You also want to be careful sizing the mortises. I have found cutting a mortise no more than 50% of the thickness of the wood is a good rule of thumb. That way you have 25% of the thickness on each side which will give good purchase for the mating glue joint. I like to set the depth to 50-75% of the width of the cross grain piece but no more than 2". Cut the tennon length to be 1/16-1/8" less than the sum of the depths in the two mortises. That will allow for a bit of space at the end of the tennon so the glue does not cause a hydraulic lock preventing the pieces from pulling together properly.
I tend to cut the mortise a bit longer than the width of the floating tennon to allow for small adjustment during final glue up. I like to thickness the tennon to be an easy slide fit so inserting it does not scrape all the glue off of the sides. The tennon will swell when surrounded by the wet glue anyway and if it is too tight can telegraph through to the assembled piece. The only time I do a tight fit is when alignment cannot easily be accomplished at glue up. The floating tennon joint is very strong anyway and with modern glues (I like Rooglue but there are several good brands available) I have never had a joint failure.
The other reason for not setting the tennons too tight into the mortise is to ease assembly when multiple parts have to come together during glue up. The ability to slightly spring one joint to assemble others can be a real help. Since we can cut perfect 90 deg edges on our pieces (thanks to the squaring fence on the CU3xx) the resulting joints will be tight and 90 degrees anyway. The tennon just adds the structural strength.
Aligning the mortises is relatively easy if you use a 90 deg. squaring stop clamped to the mortise table. Put one edge up against the registration lip at the front of the table and use the other edge to align your work pieces. You can cut one member with its end pressed against the stop and one with an edge pressed against the stop and the two parts will perfectly align outside edge to end grain. Just be sure to always orient the faces the same relative to the table; ie. I always work with my good side down on the table). That way even if your cutter is not perfectly centered on the piece, or if your pieces are not exactly the same thickness, you still will get flush edges on the good side after glue up.
If you are centering your cutter on the end grain cut then you will need to cut the corresponding long grain cut from the left on the piece on one end and from the right on the piece from the other end. To make that easy, set up the first cut by clamping the 90 deg. stop at the appropriate spot to make the end grain cut. Now press an edge of the work piece up against the stop and clamp it down. Make the end grain cut. Flip the piece around and make the end grain cut on the other end. Do the same for all the end grain pieces. Now cut all the right side cuts by placing the long grain piece with its edge against the registration lip and its end against the squaring stop. Once you have cut all the right side cuts replace one of the end grain cut pieces and clamp it down. Remove the 90 deg squaring stop and place it on the other side of the clamped work piece. Clamp it down and you are ready to make the left side cuts all the while keeping the same "good" face in contact with the table. You can make all eight of the cuts for a rail and stile assembly with just this one set up. Fast, perfectly fitting and no measurement errors to ruin your day
Hope this helps.