assembly manifest - An integral part of every assembly that
renders the assembly self-describing. The assembly manifest
contains the assembly's metadata. The manifest establishes
the assembly identity, specifies the files that make up the
assembly implementation, specifies the types and resources
that make up the assembly, itemizes the compile-time
dependencies on other assemblies, and specifies the set of
permissions required for the assembly to run properly. This
information is used at run time to resolve references,
enforce version binding policy, and validate the integrity
of loaded assemblies. The self-describing nature of
assemblies also helps makes zero-impact install and XCOPY
deployment feasible.

metadata - Information that describes every element managed
by the common language runtime: an assembly, loadable file,
type, method, and so on. This can include information
required for debugging and garbage collection, as well as
security attributes, marshaling data, extended class and
member definitions, version binding, and other information
required by the runtime. 

there isi'nt much of the difference in them 
as i can say assembly manifest is part of meta data
ie meta data contains two parts type info & assembly info

type info tells u about the ilcode , what are the function 
in it
what are the parameters it have etc
while assembly info or manifest tell u about name , size, 
version