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Ok here is the deal, I have a 2004 Honda Civic EX manual transmission. The other day with driving home the check battery, check engine light came on. Also at this time the speedometer stopped working. I immediatley took it to a mechanic as I know nothing about cars. He told me my alternator was bad and changed it to the tune of $325.00. Everything was great.... for one day. The second day as soon as I started driving the same exact thing happens. Everything seems to run ok and the lights are not dim but same gauges are on and no speedometer. So i began to research, I found on this forum some people having the same issue. I checked fuse #4 and sure enough it was blown. So I changed the fuse and as soon as I started the car it immediatley blew with the new fuse. Please if anyone has any idea as to what I need to do next please let me know. I really don't have money to pay a mechanic so it's time I learn how to fix this thing my self. Thanks

 
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Sounds like it may be shorting against the body somewhere. This controls the alternator/ELD unit so your charging system will not work which is why the battery indicator came on. It also controls the speed sensor which is why your speedometer does not work and controls the EVAP and heater on the primary/secondary oxygen sensors which will cause DTCs to be set and the check-engine light to come on.

A few areas to look:
a) if you have had any aftermarket car alarm/security system installed someone may have tapped into the black/orange wire here for an ignition connection and it may be shorting there (look to may sure that the black/orange wire looks okay from the in-dash fuse box to the wiring loom.
b) #4 fuse also powers the heater on the oxygen sensors which is another problematic area where the wire becomes exposed and shorts against the exhaust manifold or any harness. Look at the wiring to the oxygen sensors and look for any exposed or fraying on the wires.
c) if (a) and (b) do not show anything then you'll need to inspect around the speed sensor on the transmission, the EVAP purge solenoid, EVAP vent solenoid and EVAP bypass solenoid, the alternator, the ELD unit and finally the wiring harness which can be very painful to track down. A really advanced shop may have a TDR which can help enable tracking down where the exact location of any short.