Hi Frans
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- Can I use every I/O pin on the FPGA? ( so I can order my PCB )
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Yes. Provided the pin is a generic I/O and not a dedicated pin (i.e. jtag, config, ...). Quartus pin planner will guide you in connecting your signals to right pins.
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- How should I program my FPGA?
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There are many configuring options.
Usually you want to use jtag in debug phase and then a serial eprom when the board is deployed.
Refer to the documentation of the device you want to use.
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- Can I use the Altera Quartus II Web edition to program my FPGA?
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Sure.
Unless you are planing to use a big high end device (and I don't think this is your case), you can use Quartus Web Ed. for the complete design flow, from scratch to release.
Regarding your question about fpga programmable functions the answer is again yes. You can virtually program fpga for any function.
The limit is your fantasy, besides device resources.
The freq modulator and pwm you need is one of the basic function, very easy to implement.
Regards
Cris