What tool can I use to align multiple protein sequences to one reference sequence?
What you want to perform is commonly called a multiple sequence alignment.  As @Wayne_Yux said, the first step is to put all of your protein sequences in a single fasta file.  You can then use one of several online tools to apply different alignment algorithms to your protein sequence set.  

A popular sequence alignment algorithm is Clustal, which progressively builds a multiple sequence alignment from all of the pairwise alignments.  genome.jp hosts a web-based alignment tool that allows you to choose from Clustal and other alignment types (1).  For alignment of many small sequences to a single larger sequence, you should use the "SLOW/ACCURATE" option (2).  After you upload your fasta (3) and execute multiple alignment (4), an aln file will be generated which you can download (5). 



You can then take this aln file and upload it to a different tool that allows you to visualize alignments.  Personally, I like ESPript, which gives color-coded alignments in pdf or image formats.  Because you want to compare many sequences, it will probably be necessary to change the "Alignments output layout" parameters, e.g. change "Gap between blocks" to a smaller number to fit all of your sequences in one frame.