@Orome could you send us an example document via email@example.com to help us fix the LaTeX compilation issue with it? Example documents help us a lot in fixing this kind of issues. Apologies and thank you for your help and patience!
Regarding LaTeX installation: which LaTeX installation are you using? We presently support MacTeX 2013, 2014, 2015. You'll find more information here: http://support.manuscriptsapp.com/topic/10/manuscripts-latex-typesetting -- we're looking into supporting MacPorts installed version of LaTeX next (that has just come up).
It may seem like a silly restriction to have to "find" one's LaTeX installation ("why can't it just find my pdflatex or use
$PATH?") but the problem is that as Manuscripts is a so-called sandboxed OSX application, it has certain security limitations (which you really as a user benefit from because the app really cannot touch anything but the documents you have passed to it)… but it does mean that we need to explicitly guess where to find the TeX utilities the app needs to operate.
Regarding the general point of "what is it that the app does" - the idea at 1.0 is to focus primarily the content (although a lot of style information is included in the templates too). Changing the look of the article is available also for LaTeX output so you should find that for instance changing the font characteristics etc will also have an effect in LaTeX.
However, if you are writing for a journal where you must submit with a LaTeX template with a specific document class, a text editor or LaTeX IDE of some kind is probably your best choice still: supporting the entire world of LaTeX document classes -- TeX after all being technically a Turing complete programming language -- is something we would reach after 1.0 if it looks like there is a lot of demand for far more extensibility towards specific kinds of thing that can be expressed in LaTeX. Making the preamble configurable and allowing for arbitrary LaTeX blocks in the document has certainly come up in feedback already.
CEO & Co-founder of Manuscripts.app Ltd