How to annotate a .broadpeak file with 9 columns?
This is what the columns of broadPeak format mean (from UCSC):


  
  chrom - Name of the chromosome (or contig, scaffold, etc.).
  chromStart - The starting position of the feature in the chromosome    or scaffold. The first base in a chromosome is numbered 0.
  chromEnd - The ending position of the feature in the chromosome or   scaffold. The chromEnd base is not included in the display of the    feature. For example, the first 100 bases of a chromosome are defined 
  as chromStart=0, chromEnd=100, and span the bases numbered 0-99. If 
  all scores were '0' when the data were submitted to the DCC, the DCC
  assigned scores 1-1000 based on signal value. Ideally the average  signalValue per base spread is between 100-1000.
  name - Name given to a region (preferably unique). Use '.' if no name is assigned.
  score - Indicates how dark the peak will be displayed in the browser (0-1000).
  strand - +/- to denote strand or orientation (whenever applicable).    Use '.' if no orientation is assigned.
  signalValue - Measurement of overall (usually, average) enrichment for the region.
  pValue - Measurement of statistical significance (-log10). Use -1 if    no pValue is assigned.
  qValue - Measurement of statistical significance using false    discovery rate (-log10). Use -1 if no qValue is assigned.
  


And this is how the BED format looks like (from UCSC):


  
  chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or    scaffold (e.g. scaffold10671)
  chromStart - The starting position of the feature in the chromosome    or scaffold. The first base in a chromosome is numbered 0.
  chromEnd - The ending position of the feature in the chromosome or    scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined 
  as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
  name - Defines the name of the BED line. This label is displayed to    the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
  score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
  strand - Defines the strand - either '+' or '-'.
  thickStart - The starting position at which the feature is drawn    thickly (for example, the start codon in gene displays). When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.
  thickEnd - The ending position at which the feature is drawn thickly    (for example, the stop codon in gene displays).
  itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track    line itemRgb attribute is set to "On", this RBG value will
  determine    the display color of the data contained in this BED line.
  NOTE: It is    recommended that a simple color scheme (eight colors or
  less) be used    with this attribute to avoid overwhelming the color
  resources of the    Genome Browser and your Internet browser.
  blockCount - The number of blocks (exons) in the BED line.
  blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
  blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
  




So, first six columns are basically the same. The 7th and 8th column of your new BED file should be same as 3rd and 4th columns respectively. Since columns 4-12 are actually optional for a BED file you need not actually fill the rest of the columns. In any case blockCount would be zero for your case. RGB value is also not necessary. However, if whatever software you are using is asking for a 12 column file then set these:


itemRGB (column 9) = 0,0,0 (black)
blockCount (column 10) = 0


You can use whitespace in rest of the two columns. 

You can easily use any scripting language to do this. I am not going to explain how to do that because that is off-topic here.



How to find nearest genes without using Peakanalyzer?


Download the GENCODE annotation GTF file and decompress it.
Read the broadPeak file and store the locations of the peaks.
Define what the minimum level of proximity is (for e.g. 2kbp up/downstream)
Parse only those lines of the GTF where the third column="gene"
Subtract the downstream window to start and add the upstream window to stop position of the gene. Columns 4 and 5 respectively.
Gene information is stored in 9th column. 
If the stored peak position falls within the modified start/stop positions then print the 9th column. 


Again, this is has to be done programmatically. It is not very difficult. To explain how to do that is off-topic in this forum. I explained the algorithm which you can implement in your favourite scripting language.