After saving the corpus to whatever directory you'll be working in, you can start the alignment program and load the corpus from the main menu by selecting "File" and then "Open". Then go to the directory with the corpus file and select the file. When you open the alignment tool again, there should be a short cut to opening the corpus file from the "File" menu.
Please don't edit the corpus file directly, only use the alignment tool with it. Please also be sure to save often (select "File" and "Save" from the main menu). The program will ask you to save changes if you quit through the main menu but not otherwise. Make sure to save before exiting the program.
You'll send several text fields in a row with the labels "Context", "Eliciting", "Elicited", "Alignment" and "Comment". You can ignore what appears in "Context", "Alignment", and "Comment" and shouldn't edit those fields. In Eliciting you'll see an Spanish sentence or sentence fragment. In Elicited you should see the translation of that Spanish sentence. What you'll be doing is marking which words in Spanish match up best with which words in the other language.
A elicited word may align with one or more source (i.e. English or Spanish) words, or no source words at all if there is no translation of it. The same goes for the other direction. Add as many or few links as needed. Find the words that are translations of each or that serve similar grammatical roles. Links can cross each other as much as needed. Phrases can also be aligned.
To align a pair of words, click on a source or target language word, and then click on the corresponding word in the other language. A line should appear indicating the alignment, and a number pair will be added to the Alignment field. A word should be able to have as many lines coming out of it as you need. You will not be able to edit the "Eliciting" text field. Once you start adding alignments, don't make any more changes to the "Elicited" text field.
To add a phrase alignment, hold down the Control key while clicking on the words. While holding the Control key, you can click on as many Eliciting and Elicited words as you like. The words need not be next to each other in the sentence. When words on both sides have been selected, click on the "Add Phrase" button.
To delete a link, do the same process on a linked word pair (click on the Spanish and then other language word). The link should then disappear.
When you're done with a pair, you can click on the forward arrow ">" to move to the next pair. You can also go back with "<". The double arrows "<<" and ">>" take you to the beginning and end of all the sentence pairs. You can also type the sentence pair index in the field between the arrows to go there directly.
You can also search for what sentence pairs a word is in using the "Search" menu option and selecting "Word". Type in the word, select the appropriate language and click "Search". A list of sentences with the word will appear.