I am copying his notes to me exactly so that I don't misinterpret it.
"Exporting - actually I would recommend selecting a configuration and using Compile, not using Export.
I should probably get rid of Export but it's included for convenience in some circumstances.
The advantage of selecting a configuration and using Compile is that you're clear about what set of tweaks (in the configuration) will be used for this file. "Export" may have to guess a configuration, and the settings may be wrong for the file type."
So, I have to admit that in making decisions about what to include or not include in my book, I thought that explaining the "configuration" portion of Jutoh would be one step too far and that EXPORT was more easily understood by most non-technical writers. However, after an exchange with Dr. Smart, he convinced me of the importance of using COMPILE because it will look to a specific configuration to make decisions about how to create your file in the best possible manner.
So, I've added a few screen shots here and some explanations regarding some of the most common configuration options my readers will want to use. Also, don't forget that Jutoh provides a great 180 page free user guide. It will answer things in greater detail than I have her and discuss some of the options I don't cover in the book or in this configuration tutorial.
How do you get to the configuration section of Jutoh?
Go to the top menu line and select Book | Edit Configuration.
First is to make sure the formats you will want to have Jutoh create are checked. By default all the formats are checked. You can leave it that way or uncheck the ones you will not use. Definitely you want to make sure that MOBI and EPUB are checked as those are the two formats used by the majority of ereaders (MOBI for all kindles and EPUB for everything else).
Another configuration section to check is the cover. In the book I highly recommend that you create your cover separately in a good graphics program (like Photoshop) or have it created professionally. You then indicate to Jutoh you will use that cover. That cover becomes the DEFAULT cover. So, you want to be sure that Jutoh is using the DEFAULT cover.
Another important section is around optimization. Jutoh can do some special things in the background to make sure your book works the best for Apple iBooks and for Kindle. Be sure those optimize options are checked: Optimize for iBooks; Generate iBooks XML, and Optimize for Mobipocket.
There are several other options you can see if you scroll through, but these are the ones likely to be used by everyone.
Okay, I changed the configuration now how to use a Compile?
The easiest thing to do is to make the selection on your Jutoh drop down in the control panel. Note you can select epub or mobipocket (same as mobi). You might also want to specifically select Smashwords if you distribute through them, as they have some additional "quirks" they require.
Once you have made your format selection, click on the COMPILE button.
In the example above, I selected an EPUB file. Once that is compiled. I can then go back and select MOBIPOCKET for my Kindle compile without having to leave the program and come back. Then go back and select SMASHWORDS or whatever other format you wish to compile.
I hope this helpful. I have asked Dr. Smart to join us in January to answer some questions both from me and from readers, so stay tuned for that scheduling. I know lots of people will have questions to ask him or suggestions to make about the program.