In k-mer analyses (including KmerGenie), paired-end information is not used, so you can just use all your files - order doesn't matter. You have two options with KmerGenie:
1.Concatenate your fastq files:

cat hiseq_reads_ecoli_R1.fastq hiseq_reads_ecoli_R2.fastq > hiseq_reads_ecoli_R12.fastq
kmergenie hiseq_reads_ecoli_R12.fastq -l 21 -k 121 -s 2 -o out_file.txt -t 16

2.Use a reads list:

echo -e "hiseq_reads_ecoli_R1.fastq\nhiseq_reads_ecoli_R2.fastq" > reads.list
kmergenie reads.list -l 21 -k 121 -s 2 -o out_file.txt -t 16

Option 2 has the advantages that you don't need to duplicate your data and you can include as many files as you need.