Again good questions!
Always connect all the VCCs and GNDs together. This makes your Bit modular with the rest of the littleBits. (the ProtoBit gives you the option to disconnect them but I dont see a reason for that)
What you do with the SIG IN and the SIG OUT is up to you. There are in general 2 configurations.
SIG IN == SIG OUT. Put the jumper in between on the ProtoBit. In general only used for OUTPUT Bits. Use this if you only want to read (use) the SIG IN but not want to change the signal. You just connect the SIG IN to SIG OUT. (Note that it now makes no difference where you connect your circuit, on the top or on the bottom of the ProtoBit) E.g. see my RGB LEDstrip Bit: http://littlebits.cc/bitlab/bits/individually-controllable-rgbstrip-bit
SIG IN != (is NOT) SIG OUT. Remove the jumper in between on the ProtoBit. In general only used for INPUT Bits, LOGIC Bits. Use this if you want to read the SIG IN and based on that make some kind of SIG OUT.
E.g. my Radio Bit: http://pv-productions.com/radio-bit/. But also the MP3 Bit, the CloudBit, LatchBit, InverterBit etc.
Also it is possible to only do something with the SIG OUT and don’t use the SIG IN. E.g. for your pressure sensor and my NFC Bit: http://littlebits.cc/bitlab/bits/near-field-communication-nfc-bit
Hope that clears some things out:)