Thanks for writing in!
Before I answer your questions, I would like you to check this article if you have not already regarding Header and footer builder, so that you can have a good idea about the editor. https://theme.co/apex/forum/t/pro-header-and-footer-builder-introduction/103
Coming to your questions:
1- regarding the menu alignment and structure, please follow the structure I have mentioned in the screenshot below.
2- Please refer to the screenshot below to change the font/color and size of the menu.
3- To load the font family, please use template by clicking the line menu in the left corner. Then create your font template by choosing the font family and other options.
Refer to the screenshot.
After save the template go back to header editor again and edit the menu, Now you can see the font family there.
If that doesn't work please send us your login and FTP details in a secure note so that we can have a look.
4- regarding the collapsed navigation, you can make it square by changing the border radius to "0". Please refer to the attached screenshot.
Regarding the position things you can refer to the article for the content structure. If that doesn't help please send us your details as mentioned above.