It seems that if a pipe has a swale upstream then the pipe uses the Manning's equations to compute flows etc, but if it has nothing upstream or a pipe upsteam then it uses the Colebrook-White equations. This means that on the same storm water system I can have one pipe where 0.6 (ks (mm)) needs to be entered and another pipe where 0.012 (n) needs to be entered. This is confusing and could lead to big problems if 0.6 is entered instead of 0.012 or visa versa. If it was highlighted if the "ks (mm)" or the "n" was being used then that would be obvious which figure should be inputted.
This issue came up because I had to convert an upstream pipe into a swale and Flow converted all the pipes downstream to swales. When I converted them back to pipes they retained the ks (mm) from the swales of 0.033. Because they were back to being pipes I assumed that it would use the Colebrook-White equation and manually changed the 0.033 to 0.6. This then caused flooding because the pipe was using the Manning's equations. Once I noticed this and inputted 0.012 the problem was solved but I now have some pipes with 0.6 and some with 0.012 in the same system and this is asking for errors to be made. If flow highlighted which equation it was using by greying out or crossing out the ks (mm) or n on the label then it would be more obvious what was going on and easier to understand.