Thank you for your help, I was able to resolve my problem with this advice.
Less important to my project but I am curious and haven't found a clear answer here - if I tried to import my data as the wrong type (e.g. I have paired end reads with 33 quality score, what if I tried to import as another type instead), would the program continue and try to analyze the data anyways, or does the import process 'check' if the data is in the correct format? I'm also thinking about the demultiplexing steps, if I tried to demultiplex samples that were not multiplexed, would qiime refuse the command or would it make changes to the file?
My lack of experience with the program makes me worry about making accidents like this without realizing, and tainting my downstream analysis.