Aligning sequences
Note: by default, Cube will align the sequences for you. So you do not have to worry about this, unless you are explicitly worried about the quality of the alignment.
If you want to make your own alignment, one program you can use is MUSCLE. It performs fast and high quality multiple sequence alignments, including profile alignments, and can produce output in FASTA or MSF formats. More help on using MUSCLE is available on its own site or with the program itself.
Note also that you can launch MUSCLE from within SeaView, perhaps one of the most comfortable ways to use it. Just make sure to put both executable files in the same folder (directory).
  Another good program for producing multiple sequence alignments is MAFFT. The main advantage of MAFFT over MUSCLE is that it allows you to more easily customize the weights and distances between different residues and gaps. Again, more help on using MAFFT is available on its own site or with the program itself.  
To learn how to align two alignments to each other, check out the 'profile alignment' options for these two, or any other alignment program you choose to use. In both MUSCLE and MAFFT the profile alignments become a bit of a hassle if there are more than two groups involved, so Cube will do this for you.
  Wikipedia on MSA  
  MSA software on Wikipedia