I have been known to fish those waters at one time or another.
First off the St. Joe is an option, it is mainly a boaters river, any wading access (usually near dams) has a ton of fishermen. Especially during the runs.
If you are talking Salt, Little Cal, Trail, and a couple of other creeks leave the fly rod at home and bring (gasp) a spinning rod. Not saying you can't fly fish them; you can, but not as well as with a spinning rod.
All of the creeks are full of downed trees and are not that wide. The trees/brush line the banks making fly cast tough, even roll-casts are hard.
There are some places on the creeks where a 10' rod can almost touch the bank on the other side.
There is a fly shop in chesterton that has some good info on the creeks, most guys indy fish or chuck n duck with very little weight. Leave your tips at home, unless you dare to brave the St. Joe.
If you want to explore, go to Portage and grab a couple of local maps, start where the major roads cross the creeks, you will find fish. Just remember if the land is posted do not tresspass, the landowner even owns the stream bed in Indiana. So even if you are wading you are tresspassing.
E-mail or PM me if you want some off-line info, can't give you the secret spots but can point you in the right direction.