Are you asking how to install mods as well or what mods are good?
I assume you are asking for good mods.You seem to enjoy playing in U-boats I would highly recommend Operation Monsun
http://www.subsim.com/radioroom/showthread.php?t=134922 make sure that you follow the instructions to the T.I think that this mod is much better than Silent Hunter 5 overall.The files unzip into a double folder so you'll need to get rid of that or JSGME wont take them in other words it needs to be File>data file not File>file>data file.
Depending on your preference it will vary a but JSGME should look like this you must pick only one extra environment either the Med or Pacific:
OM v705
OM v720
OM v720 Patch 5
OMEGU v300
OMEGU v300 Patch 7
OM_Med_Env
Just read the page in the link there are several options for this mod that is just the basic list.
If you want to try the US Navy you should try Real Fleet Boat or Trigger Maru Overhauled or Fall of the Rising Sun.
RFB
http://www.subsim.com/radioroom/showthread.php?t=159709
TMO
http://www.subsim.com/radioroom/showthread.php?t=132330
FOTS
http://www.subsim.com/radioroom/showthread.php?t=147988