Sorry for a late reply, but I thought that You tried it already...
For example:
After installing 1.5 U-boat missions...
Install TMO, OM and Real Environment
Than:
...go to
http://www.subsim.com/radioroom/showthread.php?t=150313
and download (for example) :
Sh3toSh4[1].V3_TMO_RSRDC_OM
Just copy two files from Data\Env: EnvColors_Atl SkyColors_Atl
and paste them, accordingly, into your Data\Env folder of your basic installation (TMO, OM and Real Environment)
Always backup original files before paste...
(I like also SH3 music and speach files...)
***
If You are familiar with JGSME you can make a number of various combinations and simply "trigger" them when You want... ( for example... you leave your port in muddy coastal waters starting patrol for two days ...and during second night, you switch to open atlantic blue that appears with first light )
Various Env files could be pasted (or JGSME) in various installations... as on my second image, EnvColors_Atl & SkyColors_Atl
from OM into "TMO, OM and Real Environment installation"
Even more, You can
insert wider parts of some mods into other mod combination... 
It is up to your imagination !!!
***
From your questions, I assume that you are not experienced moders, so my
friendly advise would be:
> to examine JGSME file structure first.
Once you are familiar with JGSME engine, store your "combos" into MODS folder and use them when you want.
> always name your combo folders in a way
that it reminds you of content (mix structure) , after some time you will
forget your "content and origine" of folders...
I will
not upload any download mods because:
- it's so simple to make
- your mixing imagination could be better than mine
- don't like to upload material made by other people
I would kindly ask experienced sailors to stop laughing at these "instructions" as young sailors could not become grey wolves over night...