I am trying to write a .pcap file, which is something that can be used in Wireshark. In order to do that, I have a couple of structs with various data types I need to write
Use libpcap or WinPcap - pcap_open_dead() to get a "fake" pcap_t to use with pcap_dump_open() to specify the link-layer header type (for Ethernet, use DLT_EN10MB) and snapshot length (use 65535), pcap_dump_open() to open the file for writing, pcap_dump() to write out a packet, and pcap_dump_close() to close the file. MUCH easier than directly using fopen(), fwrite(), and fclose() (which are what libpcap/WinPcap use "under the hood").
And, yes, you have to get the byte order in the packets correct. The byte order depends on the protocol; for the type field in the Ethernet header, and for all multi-byte fields in IP, TCP, and UDP headers, they have to be in big-endian order. (The magic number in the pcap file is irrelevant to this - it only indicates the byte order of the fields in the file header and the per-packet record header, NOT the byte order of the fields in the packet, as well as, due to the way it's implemented in Linux, the meta-data at the beginning of packets in Linux USB captures. The packet data is supposed to look exactly as it would "on the wire".)