OK, going to make a few quick assumptions here:
First, I assume you are using the clock hands method to verify your initial seed. Now, if you are using the 1.0.2 version of the 3DS RNG Tool, it
should have the option Safe F only (mine does), so you may wish to check the version of your tool. Regardless, if you are doing this with the clock hands and without the assistance of the PokeCalc overlay, it is better to always tick this box since it filters out unsafe frames, which as their name implies, are not safe to be aiming for.
In the stationary RNG (Edit: Wild; made a mistake before) tab, select Blacephalon and let the tool figure out all the parameters - do not modify them whatsoever. Next, you enter the IVs/nature/Hidden Power etc. that you want into the filters then search. If you used the Gen 7 Main RNG Tool to figure out your seed with the clock hands, leave the initial frame at whatever the tool gives you (it will do it automatically if you searched via clock hands). It usually is either 485 or 486, but if you did ten hands then it would be 487 and so on. Set your upper frame limit (50,000 is usually good when you're still starting out and trying to get the thing to work).
Regarding number of NPCs, for the UBs, simply use the photos from this guide:
http://pokerng.forumcommunity.net/?t=59574488. Make sure you stand at the precise spot listed; this ensures there are 0 NPCs, allowing you to use that parameter. Since you are doing this manually, it is advisable to stick to as few NPCs as humanly possible. Even if you can't see them, NPCs may be able to affect the advancements, so ensure you stand at the precise spot indicated. When you are standing at the right spot, save then soft-reset (Start+Select+R) to begin the RNG (with the clock-hands).
Once you've searched and found a frame that you like, use the Main RNG Tool (put this desired frame, your "target" frame, in the appropriate box) to find your time, input it into the "3" column of Eon Timer's No. of frames - do not touch the Pre-Timer (leave it at 2500). Continue into the game as you start the timer, and once you are in the game, open the menu with "X" (this prevents the character from fidgeting, which is a problem in and of itself) and put the arrow over the Bag. Once the timer gets to 0, open the bag (frames do not advance whilst in the bag), get the honey and use it. Note that as you use it, the frames
will advance, but the current tool takes that into account.
Catch the Blacephalon, then take it to the PokeCenter to check IVs, nature, etc. Reset the filters (just put in the 3 perfect IVs, then set the range 0-31 for the others, put in the nature, and, if you want, the Hidden Power). Next in the far-right, click on the "Target frame +/- 100 option". Put your target frame in that box then search. With a bit of guesswork and estimation, you should be able to find the frame you actually hit. Now check the "Shift/F" column of the frame that you hit. It may be + or -; whatever it is,
add that to your target frame - note that this means a net subtraction if the "Shift/F" is a - since adding a negative number results in subtraction. For example, say my target frame was 6000. If my Shift/F is +4, then I'd get 6000+4=6004; if it was -3, then I'd get 6000+(-3)=5997. Put this number into the "Frame Hit" box of Eon Timer then hit "Update". It will update your "Lag" for you, so you don't have to mess with the Pre-Timer. Note that if there is a cluster (2+) frames that you might have hit (one after the other usually), just find the average of the Shift/F column (e.g. say I find there is a cluster of three with the stats etc. of the Blacephalon I caught, with Shift/Fs of +8, +10, +12 - I'd just go with +10 since that's the average - round to the nearest whole number obviously). Finally, soft-reset and try the RNG again, using clock-hands to find your initial seed, set your parameters, and search for a new target frame. Continue this process to "calibrate" your timer to be as accurate as possible; eventually, you will hit your desired target (it may take a bit though, my current ceiling for this process is about 8 hours).
If you cannot find the frame you hit during the searching process, then you have possibly found the wrong seed, provided you've done everything else right (such as, for example, actually leading with a Syncher...). Reset and try again. Clock hands are not the nicest thing; I advise using the starting hands and pausing your video of the clock hands
just as they appear and entering what you see - I have found that that works best.
Hope this helps, feel free to ask for further clarifications if there is anything unclear.