I have been trying to have an image or logo in the Flat only on the front page and done everything I can think. On my android when I select 'Homepage Logo' it appears on all pages. Also, I have three sub sites running, do I have to install MobileJoomla on all and the Flat template?

1. Which option do you mean, "Header Logo Image" or homepage's "Background Image"?
Do you use latest MJ and Flat versions? What Joomla version do you use?

2. Most likely yes if you have separate Joomla installations on that sites.

1. I should ask, how do I have a Homepage (Home Page Layout) that is for only the Homepage. This would include all the features (Header Logo Image, background, opacity, colors...). I want this to be the only page (Homepage) with these options and not carry through other pages. Is there a list of known third party modules/plugins that conflict and/or is there a plugin that is needed or recommended to make things work a bit better more using the Flat template?

First site is Joomla 3
Others Joomla 2.5+
Latest MJ and Flat
WOIsite.com

2. I thought so, Thanks

There are three ways two display logo on homepage only:

1. Display it in header bar using "Show in Header" and "Header Logo Image" options in "Homepage Layout Settings" section of Flat's settings.

2. Display it below header bar as a full-width image by set "Background Image" option in the same section.

3. Use MobileJoomla's "Header" module in the top mobile position (mj_smartphone_header/mj_iphone_header by default) and assign that module to homepage only.

There are other settings in "Homepage Layout Settings" section. If you need more, note that homepage has ".ui-page.home" CSS selector, so you can adjust colors of specific elements etc. in template's css/custom.css file.