I have not used annotatePeaks, but why don't you find the location of your motifs using FIMO from the MEME suite, and then use bedtools intersectBed to check which motif fall within the peak. I am assuming that you have a list of peaks as intervals (for example in bed format).

Assuming inputs (peaks and motifs) are sorted BED files, you could use BEDOPS closest-features or bedmap to associate a motif with a nearest peak or set of nearby peaks, resp. You can use the same tools to do the inverse search: to associate a peak with its nearest TF binding site or set of overlapping sites.