When you set 64-bit the resulting binary is a "Fat" binary, which contains all three Mach-O images bundled with a thin fat header. You can see that using otool or jtool. You can check out some fat binaries included as part of the iOS 7.0 SDK, for example the AVFoundation Framework, like so:
% cd /Developer/Platforms/iPhoneOS.platform/DeviceSupport/7.0\ \(11A465\)/Symbols/System/Library/Frameworks/AVFoundation.framework/
%otool -V -f AVFoundation 9:36
Fat headers
fat_magic FAT_MAGIC
nfat_arch 3
architecture arm64 # The 64-bit version (A7)
cputype CPU_TYPE_ARM64
cpusubtype CPU_SUBTYPE_ARM64_ALL
capabilities 0x0
offset 16384
size 2329888
align 2^14 (16384)
architecture armv7 # A5X - packaged after the arm64version
cputype CPU_TYPE_ARM
cpusubtype CPU_SUBTYPE_ARM_V7
capabilities 0x0
offset 2359296
size 2046336
align 2^14 (16384)
architecture armv7s # A6 - packaged after the armv7 version
cputype CPU_TYPE_ARM
cpusubtype CPU_SUBTYPE_ARM_V7S
capabilities 0x0
offset 4407296
size 2046176
align 2^14 (16384)
As for the binary itself, it uses the ARM64 bit instruction set, which is (mostly compatible with 32-bit, but) a totally different instruction set. This is especially important for graphics program (using NEON instructions and registers). Likewise, the CPU has more registers, which makes quite an impact on program speed. There's an interesting discussion in http://blogs.barrons.com/techtraderdaily/2013/09/19/apple-the-64-bit-question/?mod=yahoobarrons on whether or not this makes a difference; benchmarking tests have so far clearly indicated that it does.
Using otool -tV will dump the assembly (if you have XCode 5 and later), and then you can see the instruction set differences for yourself. Most (but not all) developers will remain agnostic to the changes, as for the most part they do not directly affect Obj-C (CG* APIs notwithstanding), and have to do more with low level pointer handling. The compiler will work its magic and optimizations.
