How you apply to colleges will depend on how you are enrolled in the programs. Both FLVS and Connections Academy are online public schools. If you are enrolled as a public school student, then you apply as a ps student with those transcripts. If you enrolled as a homeschooler, you apply as a homeschool student and only have those schools provide transcripts for the individual classes you take from them.
Either way, having an accredited diploma will not hurt you. Why would you think it would? Most homeschoolers have transcripts with a variety of outsourced classes and an unaccredited diploma.