The use of internal standard method is always more accurate than the external standard method, specially when using manual injection. An internal standard calibration has also a longer validity over time than an external standard calibration, specially when using GC/MS, since the instrument's absolute response changes over time but the relative responses remain more or less constant. 

Method EPA TO-13 does not state how many and which internal standards you have to use, it only reports a list of 5 compounds that have been used successfully as internal standards. Thus, You do not have to use all five internal standards. Normally you choose which internal standard is better suited for which analyte. For example, it is best when IS elute in relative proximity to the target analytes, and if they chemically resemble the target analytes. Therefore EPA recommends deuterated PAH for this method, since all target analytes are PAHs. Also, the five internal standards are more or less evenly distributed along the chromatogram. Thus, for every target PAH you will have a deuterated PAH with a more or  less similar retention time. You divide your target PAH in groups according to their RT, such that each group is quantified against the most appropriate IS. However, if you do not have the mix of all five IS, you might use the ones you have, and demonstrate, with synthetic samples, if the method performs within acceptable accuracy limits. 

Regarding co-elution of target compounds and IS, it is expected that this happens because the IS are deuterated PAH. However, in the Ion chromatograms there will be no overlap, since the ions of the PAH and the deuterated PAH are totally different. To quantify you use the integration of the ion chromatograms, not the TIC. 

1. Use all internal standards by their RTs

2. internal standards for MS must have higher mass then standards, but they have the same RTs - it is necessary for their ionization and using like internal standards

Internal standard method is very useful to know the relative response of the instrument for analyte. It also help in knowing recovery of the particular analyte. I think 5 internal standards are enough for use for internal standard calibration because individual internal standard can be used as representative for the other analyte as well as per EPA methods TO-13A.

Poor resolution between internal std and its target analytes are often encountered therefore to get the best result more than two injection should be performed.

The use of internal standard method is always more accurate than the external standard method, specially when using manual injection. An internal standard calibration has also a longer validity over time than an external standard calibration, specially when using GC/MS, since the instrument's absolute response changes over time but the relative responses remain more or less constant. 

Method EPA TO-13 does not state how many and which internal standards you have to use, it only reports a list of 5 compounds that have been used successfully as internal standards. Thus, You do not have to use all five internal standards. Normally you choose which internal standard is better suited for which analyte. For example, it is best when IS elute in relative proximity to the target analytes, and if they chemically resemble the target analytes. Therefore EPA recommends deuterated PAH for this method, since all target analytes are PAHs. Also, the five internal standards are more or less evenly distributed along the chromatogram. Thus, for every target PAH you will have a deuterated PAH with a more or  less similar retention time. You divide your target PAH in groups according to their RT, such that each group is quantified against the most appropriate IS. However, if you do not have the mix of all five IS, you might use the ones you have, and demonstrate, with synthetic samples, if the method performs within acceptable accuracy limits. 

Regarding co-elution of target compounds and IS, it is expected that this happens because the IS are deuterated PAH. However, in the Ion chromatograms there will be no overlap, since the ions of the PAH and the deuterated PAH are totally different. To quantify you use the integration of the ion chromatograms, not the TIC.