Perhaps look at WebLogo, which assists with making sequence logos.

You might want to look at berrylogo - it will be a more accurate means of visually comparing two motifs than a SeqLogo because a shift in nucleotide rank won't appear radically different

https://github.com/leipzig/berrylogo

Have you tried the features and annotations options in Jalview

I always liked Melina II for graphical display of the features on the sequence, and it gives a sequence logo as well. http://melina2.hgc.jp/public/index.html But if your motifs aren't identified with the selected tools they offer for "methods" I don't know if it would work for you.

I think this depends on the length of your sequence. Our MSA editor can add comments to a sequence (manually or from a file), and then a "visual summary" can show 100s of kb in a single picture. The file format takes motif name, postion, strand, colour for showing these annotations on the sequence. You can then save this file locally (BBB is Java) http://athena.bioc.uvic.ca/virology-ca-tools/base-by-base/

Hillary, W., S.H. Lin, and C. Upton. 2011. Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments, BMC Microbial Informatics and Experimentation, 1:2

William Hillary, Song-Han Lin and Chris Upton*

Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004. Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5, 96.

Cheers, Chris