C++ library path

Hello,
How to set up the path for downloaded C/C++ libraries (or, header files) so that they can be included like system headers (stdio.h or iostream)? The libraries/headers are from a package containing different folders each has different sets of headers and put in ~/Downloads/packages/sequence-master/core/include/
I was thinking two options:
1) Include the header files in my code using the double quotation, for example: #include "/home/yifangt/Downloads/packages/sequence-master/core/include/sequence/sequence.h" which looks ugly.
2)Put them in /usr/include , or /usr/local/include . I am afraid this may disturb my system.
What is the correct way, if there are better ways?
I am using Ubuntu 64bit system. Thanks a lot!

-I  /path/to/files

If the path is the current directory use

-I .
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