All right, testing this further with the template from beta 023, it looks like the template compile settings just aren’t set right because it’s been ported from the Mac and not fixed up, and as the compile pane is significantly different, the settings don’t copy over. This is something that will get fixed up, definitely, but yes, it’s not quite there at the moment.
With that, it also seems that there’s a bug inserting page breaks, as I mentioned above–neither checking “page break before” nor choosing “page break” as the separator is actually inserting the page break. I’ll drop a note about that specifically as a bug report to be sure Lee sees it.
Meanwhile, since you’re compiling to MS Word, cleaning your manuscript there really won’t be such a terrible chore, since you can use Find/Replace to whip through this. First, since the page break isn’t working, in your compile settings under “separators” choose “Custom” from the drop-down menu for the Text and Folder Separator (the last one on the list) and put some unique string there, e.g. “$$PAGEBREAK$$”. If you also want your folder/folder separator as a page break (e.g. your Part folder will be a separate page from the following Chapter folder) do the same thing in there, using the same string.
Once you’ve opened the compiled document in Word, use the Find/Replace feature to search for that string and replace it with a page break (which should be available via the “More” options in the Find/Replace pane). So that takes care of that. For the double carriage returns, run the Find/Replace again, searching for double returns and replacing with a single (also available via the “More” menu).
So that should fix your formatting now, and this should also get easier once the compile feature is debugged and inserts your page breaks correctly. 
Not entering tabs is best, yes; just use the ruler to set the indent where you want it. That way when you compile, it’s easy to change if you like by overwriting the formatting.
Double-spacing is a different issue. If you mean that you hit the return key twice, then that’s why you’re seeing it after you compile. Compile won’t remove the extra carriage return, so you’ll need to do that yourself as explained above.* In the future, you can emulate this by just changing your spacing. From the format bar, choose “Other Spacing…” from the spacing drop-down menu, and then bump up the before or after paragraph spacing to something like 8 or 10pt. That will give you the appearance of the extra line without actually inserting a character, so when you compile and override your formatting, you can easily change it without having to run a find/replace.
- At the moment it doesn’t seem Scrivener can handle this, although I may have just not figured it out for Windows. I’ll drop a note on that, too, since it’s a nice feature (and is one the Scrivener version has), to see if/when it might be available. It’s less urgent than the bug fixes, though, since it’s easily fixed in Word or other word processors after export.