Dig out your manual (if you don't have it, it's here: http://www.brother-usa.com/ModelDocuments/Consumer/Users%20Manual/UM_SQ_9000_EN_2439.PDF
We're going to do the whole "setting up a sewing machine from scratch" thing, and along the way we're going to cure your machine of its colic. My guess is you've just got a misthreading problem, but the machine may be dirty and the needle may be damaged or backwards, too.
Take all the thread off of/out of the machine. FIrst thing we're going to do is to clean the machine because lint from crummy thread or fluffy fabrics or little bits of thread that you didn't get out on previous jams can cause more jams.
Use the handwheel to raise the needle to its highest travel point. Turn to p. 70 in the manual.
Take out the current needle. When you take out the needle, check to see if the flat back of the needle (the part that goes up in the clamp) is to the back of the machine. If it's not, make yourself a note... flat of the needle to the back of the machine. If it's wrong way around, the stitches don't form properly and the machine can't pick up loops of bobbin thread. Needles that are slightly bent (ever so slightly bent!) or dull (especially if you've heard that "clunk" as it hit the presser foot) also don't sew well.
Also take off the presser foot holder, and finish the steps on pp. 70-71 for cleaning the bobbin case assembly. Use a vacuum, not compressed air, because you don't want to blow lint in further. Make sure you get rid of any bits of thread that have worked their way down. Reassemble per the manual.
Turn to p. 21 of the manual. For our purposes, it's best if we test with a size 80/12 needle (80 and 12 are the same sizes, just different numbering schemes). A size 80 needle will sew virtually every garment weight fabric, and we're going to give this machine every advantage possible right now.
Insert a new needle, flat side to the back of the machine. Make sure it's completely up in the needle clamp and tighten the needle clamp completely. Easiest way is to push up on the needle shaft while you're tightening the clamp.
Next, take a look at the bobbin you took out. Is it smoothly wound, no loops hanging out? If not, strip off the old thread and rewind the bobbin, following the instructions on p. 12-13 Wind bobbins at slowish (1/3-1/2) steady speed-- this helps keep the thread from stretching or stretching unevenly and causing tension problems and puckers. Put the bobbin in the bobbin case and continue to work through pp 14-16. Make *sure* the bobbin is going in the bobbin case right way around (thread pulls off clockwise) (this causes tangles if it's not correct) and that it's under the tension spring on the bobbin case (which will cause little loops of thread on the top surface of the fabric, and sometimes tangles.)
Next is the upper threading sequence, pp. 18-19. Be sure the presser foot lever is UP when you thread the top. Raising the presser foot opens the upper tension so the thread can actually get in there. (I suspect this was your main problem -- it causes no tension on the thread and big loops on the underside of the fabric.). Thread the needle.
Now raise the bobbin thread with the top thread: page 20 of the manual.
Pull both the top and bottom threads under the presser foot and behind the foot, over to the right.
Find a scrap of (preferably woven) fabric to test on. Set up for a straight stitch of a medium length.
If you've played around with the upper tension, set it to 4. This is normal tension for most fabrics, most stitches. If you have to adjust outside the range of 3 to 5 to get nice stitches, chances are the machine is dirty or misthreaded.
Here's how you're going to start each and every seam from now on:
1. Raise the presser foot if it's not up already.
2. Put the fabric under the presser foot, and use the handwheel, pedal (if it's got a stitch at a time function) or needle up/down control to drop the needle into the start of the seam. (If you use the handwheel, be sure you turn the handwheel in the direction that causes the fabric to feed from the front to the back of the machine. Going the other way will cause jams in some machines.)
3. Drop the presser foot. (If the presser foot isn't down when you start to sew, there's no tension on the upper thread and you get thread wads on the underside of the fabric.)
4. Hold the ends of the bobbin and top thread behind the presser foot and take a couple of stitches. As soon as you've got a few stitches made, you can drop the thread ends. This prevents thread wads at the beginning of the seam.
Executive summary:
1) Keep it clean
2) Make sure you've got a good needle, right way around.
3) Use good thread
4) Make sure the machine is threaded properly
5) Make sure you start the seams correctly.
Examples of what misthreading does to well behaved machines: http://www.picturetrail.com/sfx/album/view/22521551