Assuming that the secondary fermenter has been sitting still throughout the conditioning weeks, all of your augments should have settled to the bottom. Some stuff floats at the top, even when they've been wet for weeks, but most things sink.
To setup for bottling, bring your bottling bucket to the secondary fermenter without moving the fermenter or otherwise disturbing the settled materials. Then with the bucket sitting beneath the fermenter, insert the siphon's intake hose into your brew, being careful not to let it touch the settled materials. Move slowly so that the hose's movement doesn't cause currents in your brew as these can also resuspend settled particles. Try to keep the hose's intake pointed up towards the top of your brew, or at least horizontal to the surface, this will help keep the currents flowing into the intake, away from the settled particles.
You will want to siphon your beer from the clear middle zone, above the settled augments but below anything floating on top. If you are careful, you should be able to siphon off most of your beer without adding any particles to the bucket. Once you get most of the clean beer into your bucket, stop there. In this technique, you will only be bottling what is in your bucket at this point.
Yes, you are leaving some good beer behind in the fermenter, but you are also investing your bottling efforts into only the best of what you've made. These bottles will be very clear compared to your first batch. There are other things you can do to increase the clarity even more, such as adding geletin, but good transfer technique is where clear beer begins.
It is important that you keep the secondary fermenter perfectly still for about a week before you start the transfer, to let any suspended particles settle. So, long before bottling day, you need to place your secondary fermenter up on something stable, at a height where the bottling bucket can sit beneath it. Siphoning only works down hill, so the brew in bucket will only rise to the level of the opening in the intake hose. Keep that in mind when you situate your secondary fermenter for this task, a week before bottling day.
The next step after transferring the clean beer into your bottling bucket is to dump the rest of your beer into a large glass or clear plastic pitcher. Don't worry about all the sediment you have mixed up into this beer during the "dumping" process. It may look like pond water, but it will be drinkable again soon. Put this pitcher in your fridge and let its contents settle while you bottle up the clean beer. By the time you are done, most of the suspended stuff will have settled, so you can carefully pour yourself a cold brew. This won't be as clear as what you bottled, but it should be drinkable. If it is too gritty, put a coffee filter in a large funnel and pour from the pitcher, through the funnel, into your glass. With a little patience (and tolerance for grit), you should be able to recover most of your unclean beer.
