Multiple diacritics on one character

I suggest you to use XeLaTeX with UTF-8 encoding and fontspec for direct character inputing. Charis SIL and Brill fonts are enhanced so as to handle diacritic stacking. SIL distributes an IPA keyboard which lets you enter diacritics or you can use the Characters Map in windows.

Here's a code sample with output.

\documentclass{article}
\usepackage{fontspec}
   \setmainfont{Charis SIL}

\begin{document}

ẵ̊́ b̥̩̬̪

\end{document}

Using the tipa package, \textipa{\u=a} yields

This is well suited for a stack. Here, I set a \={} atop a \u{a}, such that the baseline of the former is 0.4pt above the nominal baseline. You may tweak that value, as I have done in the second combination, if you want separation between the diacritics.

Other diacritic combinations pose no problem, using the same technique.

\documentclass{article}
\usepackage{stackengine}
\begin{document}
\renewcommand\stacktype{L}
\stackon[0.4pt]{\u{a}}{\={}}\ 
\stackon[2pt]{\u{a}}{\={}}
\end{document}  

If one wanted the macron on the bottom, the one would stack \u{} atop \={a}.