You will need to edit the file: sbinit.config
It is located in: \Steam\steamapps\common\Starbound\win32



Next you need to open it with Notepad++
Link to Notepad++[notepad-plus-plus.org]




Next open up the location of the workshop mods
Folder Location:\Steam\steamapps\workshop\content\211820


Now in the sbinit file you need to add the line:
"..\\..\\..\\workshop\\content\211820\\*********\\" Replace the ***** with your mods name.

Make sure to put a comma after the Mods Line then after each one you add except for the last line. The last line does not need a comma. It will look like the image when its done.

Once in starbound make sure to go into the options and tick asset-mixmatch. So far this is the best working way. The advanced shortcut way makes it difficult to work on the computer hosting and copying each file in the mod folder means the mod cant get updates. However for me the Glados mod does not work for this and I haven't figured out why that one out of the 117 I have is the one that doesn't work. If figure it out I'll post why.