***Update: YN-560II is able to sync with Nikon CLS without limits. See here***
BACKGROUND (you can skip this if you just want to know how to get the YN-560 to sync :) ):
I got the YongNuo YN-560 to supplement my Nikon SB800 (controlled by my Nikon D300's popup). I knew the YN-560 was a manual flash that wasn't controllable by the pop-up flash as commander, but I didn't mind. I planned to control the SB800 remotely while allowing the YN-560 to function in manual mode for special effects like background light, rim light, etc. It seems other photographers had the same plan (see here for example). Finally, someone was able to do it. I ordered the YN-560 and when I finally received it, that was the very first function I tested.
Unfortunately it didn't work. I thought it was just unreliable, so I tried a few times. Nope -- not only did it fail to sync, it didn't fire at all. I tried various settings, such as changing the popup from inactive to TTL to Manual, and the SB-800 from TTL to AA (auto aperture) to Manual. I tried reassigning the SB-800 to Group B instead of group A, activating and deactivating Group B, switching between the 4 available channels. Nothing seemed to work. Regular slave mode did work of course (where the YN-560 does not ignore preflashes), but that wasn't enough for me.
I was able to contact the photographer who was able to trigger it and he said his popup was on commander mode but inactive (i.e., not contributing to exposure) and he was able to trigger the SB-600. However, I didn't know the exact settings.
I finally resolved to try some more combinations of settings. After a couple of hundred test shots I was ready to give up. Then I tried to figure out what exactly was going on with the YN-560. Why wasn't it firing at all when the popup was on commander mode? I then hypothesized that when the YN-560 detects a preflash, it will "hold its breath" for a specific time limit, and within that time limit, the YN-560 will ignore preflashes and watch for the "real" flash. However, if preflashes last throughout the duration of that time limit, the YN-560 gives up and shuts up, until it can restart the cycle after a pause. ***That's just a hypothesis. It's not necessarily correct.***
Based on the hypothesis, I thought the commander preflashes were exceeding the time limit for detecting the real flash. I can't shorten the preflashes, but I thought about allowing giving the cycle time to reset by using a combination of FV Lock, rear curtain sync, and a slow shutter speed. Guess what? It worked. That gave me hope to try out some more settings.
THE RULES FOR SYNCING THE YN-560 WITH CLS AWL:
Assumptions: the user wants to use a flash in commander mode to adjust a CLS AWL-compatible flash (either TTL, AA or M) while using the YN-560 manually in digital optical sync (S2 mode). Only one CLS group was tested.
Testing conditions: Nikon D300 with popup flash as commander, one SB800 as CLS slave (set to 105mm zoom), one YN-560 (set to 105 mm zoom). Dark ambient conditions (i.e., optimal triggering conditions). I aimed the two flashes about 3 feet from a wall. The YN-560's sensor (in the body) was aimed at the wall. The SB-800's cls sensor was facing up. To facilitate differentiation of output, The flashes were at different vertical positions. In addition, the SB-800's sound was turned off (because in my experience the SB-800 triggers very reliably), while the 560's sound was turned on.
Here are the convoluted conditions for the YN-560 to sync correctly with the Nikon CLS Advanced Wireless Lighting, as far as I can determine.
1. The variables that affect sync are:
a. the flash sync mode
b. shutter speed
c. the flash exposure mode of the popup and the CLS slave
d. whether FV lock is used
e. whether the slave is assigned to Group A or Group B. Group C not tested.
f. whether Group B is inactive or not. Group C not tested.
g. the channel being used.
2. The easy stuff:
a. FLASH SYNC MODE: The camera has to be set to rear curtain sync. Front curtain will not work. Red eye will not work. Slow sync by itself will not work. Slow rear sync may work if the resulting shutter speed is 1/10 or faster. Note that if you select rear curtain while in P or A mode, slow rear sync will automatically be selected.
b. CLS SLAVE GROUP: assign the CLS slave to Group A. The CLS slave can work in Group B but under fewer conditions. I didn't test all the combinations.
c. CLS CHANNEL: use Channel 1. Channel 2 and others work, but under fewer conditions. I didn't test all the combinations.
3. The weird stuff:
a. In all cases, shutter speed has to be 1/10 or faster. Any slower and it won't sync.
b. The fastest shutter speed depends on the flash exposure mode of the popup and the CLS slave. General rule: the fastest shutter speed is 1/125. I haven't been able to sync at 1/160 or faster. Exceptions to the general rule:
i. if the popup is on TTL, then FV lock is needed to sync at 1/125. Otherwise, the fastest shutter speed is 1/100.
ii. if the CLS slave is on M and the popup is on either inactive ("--") or M, then the fastest shutter speed is 1/60.
See this spreadsheet for a summary: http://spreadsheets.google.com/ccc?key=0AoRnW2_ZeadSdEZPY2VCRHBxaHVnRTJQZXJwX1p5OHc&hl=en&authkey=COmm5uMF
4. The good news: If the rules above indicate that a sync is possible, then on each occasion I've tried, the popup and CLS slave can each be adjusted, and FV Lock will work (where applicable).
As an alternative to the foregoing, it is of course possible to use the YN-560 in S1 (regular optical slave mode), while the other flashes are in Manual or Non-TTL Auto mode. Another alternative is to use the YN-560 in S2 mode, the popup on regular TTL, and an SB-800 or SB-900 in SU-4 optical slave mode.
Please check out the update on the YN-560 re sync speed and other interesting info.