To align sequences using a webserver, open the FASTA file in your browser or in Notepad, and paste the sequences into the sequence box. You can select the scoring matrix (BLOSUM, identity) using the Weight Matrix dropdown-menu in Step 2 and Step 3 (click on more options). For simplicity use the same matrix in pairwise and multiple alignments. Always use ClustalW's slow or full alignment algorithm, and not the fast one. You can compare the alignments using JalView (when the alignment is done, JalView is available via Results Summary page). Click the Show Colors button to color the amino acids according to their properties. This will also make it easier to compare the sequences. Remember that the differences between alignments are in the gaps! So focus on the gaps, heads and tails.