Any ATS system nowadays can simply work with Word or PDF file types. It will analyze out important bits of information and populate the database with your name, address, skills, employment history and related keywords. It will as well reserve the résumé in the form you submit to be viewed by the recruiter.
Lines, text boxes and color can be handled by nearly every ATS these days. Use these elements sensibly.
Warning! Be careful about using graphics as your resume may appear fake. Different ATS systems differ in their capacities to deal with images. Irrespective, words entrenched in graphics won't be documented or analyzed out. If you submit a graphic-heavy résumé, it may lose the visual appeal for which you go all-out for. As a replacement for, it may be perceived as nonsense on the other side.
ATS systems regard for definite items to be in specific places on your résumé. For instance, your name and contact information must be at the top – not placed in a vertical text box along the side of the page. Use suitable headings for the different sectors of your résumé and have them arranged logically.
Don't try to game the system. For instance, don't unnecessarily repeat the same keywords in your résumé just to get a better keyword-scoring match. It does not work that way. It may be seen, but recruiters usually take a negative opinion of this practice.
Make certain your résumé validates that you are well suited for the positions for which you are applying or else it will appear to be a sham. It is not the fault of the ATS if you are continually rejected for positions for which you don't qualify.
Use common sense. Don't apply for extensively diverse positions within the same company. And don't go for positions at significantly different expertise or experience levels within the same company, either. Remember that your whole profile will be seen by anyone in the company who is looking at your résumé.
Always review your resume before sending it to employers!