Both the runMapping and runAssembly programs are able to take in reads from other platforms, at least Sanger reads and Illumina reads. As long as the reads are in fasta format, with an optional quality file, newbler accepts and uses these reads. When the fasta files contain paired end (mate pair) reads, newbler can actually be made to use the pair information.
In general, it is a good idea to clean your fasta sequences before adding them to newbler: remove vectors, linkers, low quality parts of reads, or entire low quality reads first.
Also note that, while for sff files a symbolic link is generated in the assembly or project folder (still present after the program is finished when the -nrm flag is set), fasta files are not included in this way.