Ok, AutoGK is very self explanatory, and very easy to use. I suggest u use that if u haven't done any encoding before.
If u want to use MeGUI (imo best tool out there for encoding), then here is a basic outline of the procedure.
(if ur converting not from dvd, and something else instead, go to step 2, and skip step 3.)
1. Rip ur dvd onto HDD. Do this with DVD decrypter. Use IFO mode. If dvd dycryptor doesn't work, (some very new dvds have new protection technologies) then use rip4me.
2. Install MeGUI and update it, so u have all the newest tools.
3. Go to tools»dv2 creator. select the vob file u ripped previously that u want to convert. Select the audio tracks u want, hit queue. Close the dv2 creator, and in the que tab of MeGUI, click start, and wait for it to finish.
4. Go to tools»Avisynth Script creator. Under video input, load the dv2 file (or any other video input, such as divx). Change the cropping and resizing value is u want, Go to the filters tab, select "source is anime" if that's what it is. Click analyze and let it do it's job. If ur source is interlaced, under de-interlace, select TomsMoComp for best quality, but that requires ur output width and length both to be multiples of 4. Otherwise, use LeakKernal. change resize filter to lanczos. Click save when all that is done.
5. Back at the input tab, under video encoding, avisynth script, select the previously made one (if not done automatically for u) set/change ur video output, select ur codec, and profile, or make ur own profile, and then hit queue.
6. Under audio, do the same as for video previously. Hit queue.
7. Click on the queue tab, click start, and do something else while it encodes.
8. After it finishes, go to tools»muxer»mkv muxer (mp4 if u want to use that container instead, but mkv supports more stuff.) Select all your inputs, hit queue, go back to queue, and hit start. Wait until it finishes, and everything is done. :)
If u want subtitles, use the vobsubber tools under tools in megui. If u want chapters, under DVD decryptor, select the option to create a chapter file (ogm style) when decrypting, and then during the muxing stage, select the chapter file.
Ok, this is very messy and crappy, and no-one will probably understand what I'm going on about, but that's basically the general process of using MeGUI.
If that is way too complicated, just use AutoGK.