This is a walkthrough of how to make a collection from start to finish.
First find something you're interested in working on — a video, an audiobook, a song. Then find its Japanese text and hopefully its translation. This walkthrough will use a video and Japanese closed-captioning as the example. You can find some of those at D-Addcits and Jdrama.cc.
Download the Japanese SRT and load it into Kikuyu
by clicking File → Translate → Source file.
Now would be a good time to create the collection
You don't have to though...anyway, you can do that by clicking Collection → add to new collection. Kikuyu will make the quantum files.
Next load the video or audio
by clicking the load media button and browsing to the file.
Now would be a good time to associate the audio or video with the collection
You don'thave to though...anyway, you can do that by clicking Tools → Extract audio from current video. Kikuyu will confirm this with you and proceed to launch Virtual Dub. Agree to VDubs licensing and it will extract the audio from the video. After a minute or two Kikuyu will update the quantums in the collection with the appropriate information.
After doing this an audio file will be placed in My Documents\Kikuyu\Media. Next time you load the collection it will load the audio from there. You will have to load the video manually, or you can copy the video to the Media folder and it will automatically use the video instead. Quantums will only use the Media folder because of their sharing nature. If you have a video in D:\Movies\Japan\Mokuyou 9\2007, this probably won't make sense on someone else's computer.
At this point you have a collection with no translations. So you'll want to start translating!
Simply type the translation in the Target Language box and move on. There's no need to save anything, as the changes take effect once your cursor leaves the Target Language box. Same for the Source Language.
Drag words
Drag words to the textbox next to the magnifying glass to have them looked up in the dictionary and the recollections engines. English and Japanese can be used at the moment, the framework is there for more languages in the future. As a side-note, you can drag from any program, not just Kikuyu —so I plan on making a minimalistic mode for times when you only want a quick dictionary and don't have access to the web.
Sometimes you will find that you need to adjust the timing for a line to better match the audio
To do this click the line that you want to adjust. Update the times and click commit changes. Unlike the translation boxes, you must click commit changes to permanently save a change in the timing.

The start and finish time boxes can be edited manually, or you can double click them to set them to the time displayed in the current position box. The formats is HH:MM:SS,ms (no, I am not European). Try to take advantage of double clicking the boxes, this can save some time. For example, if the finish time is too long, click pause where you want it to stop, then double click the finish time box.
Other times you will find that a sentence has been carried over to two or more lines
Working in a collection, you can cut and paste, and use Edit → Delete line on the now blank lines.
Not working in a collection (editing SRTs in translation mode), you can merge lines together by clicking Edit → Merge with previous line to merge lines. Using the picture above as an example, line 1 will become <ルカ。元気ですか?> こんにちは。Line 2 will remain the way it is, this is because there is no undo feature at the moment and more importantly no way to insert a new line, yet. You can delete line 2 though, by selecting it and clicking Edit → Delete line.
Once you've finished
If you feel that the translations are of a high enough quality to add to the SRS engine, you can do so by clicking Collection → Add collection to SRS.
Or, consider sharing your collection by clicking Community → share your collections, and following the steps.1
Even if you feel that your work isn't good enough for someone to commit to studying, sharing your collection will allow people on the web to search for a Japanese word and hear it used in a sentence.
They may not even be interested in the translation. Or, someone could use your collection and retranslate it, but you've saved them all the hard work on correcting the timings! Either way consider it, it will only be appreciated, and sharing is anonymous anyway.
1. This page is written as if Kikuyu is out of the initial beta and has all of the planned features.