How to choose where files go in Ubuntu 16.04.

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I am new to Linux (from Windows). Is there a way to choose where files go in Linux? Windows has a "Save As" option where you can choose which drive and which folder to save that file in. Does Linux have that option?
Also, If my Linux / partition on my C drive is getting low on space, can I start saving files to my E drive? Do I need to create a separate partition for my E drive as not to interfere with my Windows files?
One final question: Can I create partitions through Windows Drive Manager, then use those partitions for Linux?
Or am I getting this completely wrong...
Any help is appreciated, thanks :)
 
"Save As" is an option provided by applications rather than the operating system. Almost all Linux applications will let you chose where you want to store data files, although normally this would be in your home directory.

Linux doesn't have the concept of drive letters. You "mount" partitions so that they appear as directories under the one filesystem tree. I would recommend keeping Windows and Linux partitions separated as far as is practical, but you can mount Windows partitions in Linux (but not, without additional software, the other way round). You can't create Linux format partitions in Windows so, if they are to be used by Linux only, they should be created within Linux.

I would recommend that you are a little careful when mounting Windows drives in Linux. You no longer have the protection afforded by Windows and it would be very easy to delete or overwrite files that are essential to the operation of Windows.
 
Thanks, I am thinking of completely redoing my Linux partitions. I want to have a set up with Linux as one partition on my SSD and all my files on another partition on my HDD. I am thinking of using a 30 gb partition for / mount point which is Linux I believe, and 20 gb for swap (read somewhere that swap should be a bit more than RAM size, I might upgrade to 16 gb). I think I will put swap and Linux on my SSD because swap feels like it should be part of Linux. Which mount point should I use for all my non Linux OS files? I believe it is home but I am not sure. I think I am going to give it a partition of 200 gb on my HDD. Is this a good setup? Any suggestions?
And how should I delete and remake my partitions? Should I delete my partitions using Windows drive manager and make new partitions with Ubuntu install?
Any suggestions are appreciated :)