marcoval,
Well, the easiest way to connect your joystick to the PC is through an encoder board like the I-pac. An encoder actually sends the keyboard strokes to the PC. For example, when you move the joystick up, the encoder will send an 'up arrow' to the PC. This, provided your wiring is correct and you are using the default MAME setting or have the encoder programmed accordingly. Whatever action is programmed for the 'up arrow' key will result. There are other options but if you have an I-pac, I see little need for doing any bypassing.
If by 'each joystick' you mean a joystick for a different player, then yes each one will use up 4 slots. If you are using say 2 sticks for player 1 (1 dedicated 4-way and 1 dedicated 8-way), then you will only need 4 slots as they can both use the same connections simultaneously. You won't be using them at the same time so only 1 will be signalling.
The I-pac2 will give you plenty of inputs if you want to build a 2-player panel with 6 or 7 buttons per player. Once again, you are not necessarily limited to two sticks depending on what your intended use vs. your design is. A fully equipped 4-player panel will require the I-pac4 (more inputs).
Does this answer your question?