One of Enhanced Economy's features is that you can read prices from a text file, which will then store the new prices in your savegame. EE comes with a number of such price files to choose from, and you can edit any of them in your favourite text editor before (re-)loading them. As an example, here is the start of "ACs realisticaly priced clutter.txt"
ACs realisticaly priced clutter.Increase the price of vanilla clutter, especially on the higher-class clutter.[Oblivion.esm]01F1E2, 1, LowerJugTan04, Tan Jug0104C9, 1, LowerClassCup03, Stone Cup01BBCA, 1, PaintBrush06, Paint Brush
If you want a Paint Brush to be worth 2 gold, just change the 1 to 2.
Another EE feature, which is accessed from EE's ingame menu as part of the Local Economy feature, is that you can choose to change the price of all items (even added by other mods) of a specific type. Say you want all alchemy ingredients to be worth 50% more, open the Local Economy places menu, choose the "Base Multiplier" and set the multiplier value for "Ingredient" to 1.5. After that, all ingredients will be repriced.