NetPositive stores a default window size and position, recorded at the moment you close the last instance of all currently open Net+ windows. Therefore, when you tap Alt+N or Alt+L to launch a new NetPos window, it will appear in the size and position of the first opened window, not the one you’re currently staring at.
When closing NetPositive, make sure the last window you close is sized and positioned exactly as you like it. New Net+ windows will then appear with the same size and position.
If you don’t want NetPositive to save the last window position every time it quits, use the tip Access hidden NetPostitive settings to turn off the „SaveWindowPos“ setting. In this case, open a Terminal window and type:

rmattr SaveWindowPos ~/config/settings/NetPositive/settings
addattr -t bool SaveWindowPos false ~/config/settings/NetPositive/settings

That way, if you get your „perfect“ window position, you can turn off the preference to save it in the future, and it will be preserved forever.
For the brave, you can manipulate the window rectangle directly through the „DefaultBrowserWindowRect“ preference, though you’ll have to manipulate a RECT attribute to do so. Good luck.
There’s the usual caveat to not make business decisions based on these preferences always being there in this form; they are subject to change in the future.
In a future version (probably R5), the secret preferences will no longer be secret: there will be some sort of UI to set all of them; though the more arcane ones will likely require an extra step to get to them, so as not to confuse non-power-users.